Two-dimensional assembly of giant molecules

This mini review summarizes recent progress on two-dimensional (2D) self-assembly of giant molecules. Two critical factors with significant impact on the formation of nanostructure are highlighted, i.e., the dimensional constraint of 2D geometry, and the conformational constraint imposed the rigid molecular nanoparticles (MNPs). Diverse 2D nanostructures have been fabricated in condensed state and solution by rational molecular design. The collective secondary interactions between functional groups on the periphery of the MNPs and their persistent shape, together with the dimensional limit, change the free energy landscape and lead to unconventional nanostructures. The unique molecular properties of giant molecules endow these 2D structures with promising technological applications.     

Design magnetischer Materialien: Chemie der Magnete

The field of molecular based magnetism is an active area of research directed toward the design of new magnetic materials. The idea is to introduce molecular strategies in magneto-chemistry. This can open completely new synthetic routes to materials with previously unknown physical properties. Spin carriers used within this approach range from purely organic radicals to metal complexes and organometallic compounds. The design of new magnetic materials with tailor-made properties requires a detailed knowledge about the interactions between possible spin carriers and the strategies necessary to achieve interactions in all three dimensions. The latter is closely related to the field of crystal engineering. Starting from introductory remarks to magnetochemistry the underlaying concepts for the design of magnetic materials on the basis of molecular compounds as well as new developments and possible applications are described.     

Supramolecular polymers fabricated by orthogonal self-assembly based on multiple hydrogen bonding and macrocyclic host–guest interactions

Supramolecular polymers constructed by orthogonal self-assembly based on multiple hydrogen bonding and macrocyclic host-guest interactions have received increasing attention due to their elegant structures,outstanding properties,and potential applications.Hydrogen bonding endows these supramolecular polymers with good adaptability and reversibility,while macrocyclic host-guest interactions give them good selectivity and versatile stimuli-responsiveness.Therefore,functional supramolecular polymers fabricated by these two highly specific,noninterfering interactions in an orthogonal way have shown wide applications in the fields of molecular machines,electronics,soft materials,etc.In this review,we discuss the recent advances of functional supramolecular polymers fabricated by orthogonal self-assembly based on multiple hydroge n bonding and host-guest interactions.In particular,we focus on crown ether-and pillar[n]arene-based supramolecular polymers due to their compatibility with multiple hydrogen bonds in organic solution.The fabrication strategies,interesting properties,and potential applications of these advanced supramolecular materials are mainly concerned.     

Binding of novel fullerene inhibitors to HIV-1 protease: insight through molecular dynamics and molecular mechanics Poisson–Boltzmann surface area calculations

The objectives of this study include the design of a series of novel fullerene-based inhibitors for HIV-1 protease (HIV-1 PR), by employing two strategies that can also be applied to the design of inhibitors for any other target. Additionally, the interactions which contribute to the observed exceptionally high binding free energies were analyzed. In particular, we investigated: (1) hydrogen bonding (H-bond) interactions between specific fullerene derivatives and the protease, (2) the regions of HIV-1 PR that play a significant role in binding, (3) protease changes upon binding and (4) various contributions to the binding free energy, in order to identify the most significant of them. This study has been performed by employing a docking technique, two 3D-QSAR models, molecular dynamics (MD) simulations and the molecular mechanics Poisson–Boltzmann surface area (MM–PBSA) method. Our computed binding free energies are in satisfactory agreement with the experimental results. The suitability of specific fullerene derivatives as drug candidates was further enhanced, after ADMET (absorption, distribution, metabolism, excretion and toxicity) properties have been estimated to be promising. The outcomes of this study revealed important protein–ligand interaction patterns that may lead towards the development of novel, potent HIV-1 PR inhibitors.     

Molecular modeling of class I and II alleles of the major histocompatibility complex in <Emphasis Type="Italic">Salmo salar</Emphasis>

Knowledge of the 3D structure of the binding groove of major histocompatibility (MHC) molecules, which play a central role in the immune response, is crucial to shed light into the details of peptide recognition and polymorphism. This work reports molecular modeling studies aimed at providing 3D models for two class I and two class II MHC alleles from Salmo salar (Sasa), as the lack of experimental structures of fish MHC molecules represents a serious limitation to understand the specific preferences for peptide binding. The reliability of the structural models built up using bioinformatic tools was explored by means of molecular dynamics simulations of their complexes with representative peptides, and the energetics of the MHC-peptide interaction was determined by combining molecular mechanics interaction energies and implicit continuum solvation calculations. The structural models revealed the occurrence of notable differences in the nature of residues at specific positions in the binding groove not only between human and Sasa MHC proteins, but also between different Sasa alleles. Those differences lead to distinct trends in the structural features that mediate the binding of peptides to both class I and II MHC molecules, which are qualitatively reflected in the relative binding affinities. Overall, the structural models presented here are a valuable starting point to explore the interactions between MHC receptors and pathogen-specific interactions and to design vaccines against viral pathogens.     

Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning

Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accurate approaches is based on a Buckingham-type approximation that uses the multipole moment expansion of molecular/atomic charge distributions. In the mid-1980s it was shown that the pseudoatom model commonly used in experimental X-ray charge density studies can be easily combined with the Buckingham-type approach for calculation of electrostatic interactions, plus atom-atom potentials for evaluation of the total interaction energies in molecular systems. While many such studies have been reported, little attention has been paid to the accuracy of evaluation of the purely electrostatic interactions as errors may be absorbed in the semiempirical atom-atom potentials that have to be used to account for exchange repulsion and dispersion forces. This study is aimed at the evaluation of the accuracy of the calculation of electrostatic interaction energies with the Buckingham approach. To eliminate experimental uncertainties, the atomic moments are based on theoretical single-molecule electron densities calculated at various levels of theory. The electrostatic interaction energies for a total of 11 dimers of alpha-glycine, N-acetylglycine and L-(+)-lactic acid structures calculated according to Buckingham with pseudoatom, stockholder and atoms-in-molecules moments are compared with those evaluated with the Morokuma-Ziegler energy decomposition scheme. For alpha-glycine a comparison with direct "pixel-by-pixel" integration method, recently developed Gavezzotti, is also made. It is found that the theoretical pseudoatom moments combined with the Buckingham model do predict the correct relative electrostatic interactions energies, although the absolute interaction energies are underestimated in some cases. The good agreement between electrostatic interaction energies computed with Morokuma-Ziegler partitioning, Gavezzotti's method, and the Buckingham approach with atoms-in-molecules moments demonstrates that reliable and accurate evaluation of electrostatic interactions in molecular systems of considerable complexity is now feasible.     

A molecular model for epsilon-caprolactam-based intercalated polymer clay nanocomposite: Integrating modeling and experiments

In studying the morphology, molecular interactions, and physical properties of organically modified montmorillonite (OMMT) and polymer clay nanocomposites (PCNs) through molecular dynamics (MD), the construction of the molecular model of OMMT and PCN is important. Better understanding of interaction between various constituents of PCN will improve the design of polymer clay nanocomposite systems. MD is an excellent tool to study interactions, which require accurate modeling of PCN under consideration. Previously, the PCN models were constructed by different researchers on the basis of specific criteria such as minimum energy configuration, density of the polymer clay nanocomposite, and so forth. However, in this article we describe the development of models combining experimental and conventional molecular modeling to develop models, which are more representative of true intercalated PCN systems. The models were used for studying the morphological interactions and physical properties. These studies gave useful information regarding orientation of organic modifiers, area of coverage of organic modifiers over the interlayer clay surface, interaction of organic modifiers with clay in OMMT, interaction among different constituents of PCN, conformational and density change, and actual proportion of mixing of polymer with clay in PCN. We have X-ray diffraction and photoacoustic Fourier transform infrared spectroscopy to verify the model.     

Mechanism of DNA-drug interactions

Over the last two decades many strategies have been planned to design specific drugs for rare diseases to target their action at the DNA level. Advancements in our understanding of the interactions of small nonpeptide molecules with DNA have opened the doors for “rational” drug design. Special methods have now been developed to give accurate account of the precise location of ligand-DNA adducts on target DNA. We are now in a position to think of designing ligands that recognize particular sequences of base pairs. This work will allow us to enter into a new era of gene therapy for diseases like Cystic fibrosis, Alzheimer’s disease and many related disorders at genetic level. These ligands can also be employed in the treatment of various types of cancers. They may also be useful as highly specific probes to locate particular sequences in the genomic DNA.     

Point charge representation of multicenter multipole moments in calculation of electrostatic properties

Summary Distributed Point Charge Models (PCM) for CO, (H₂O)₂, and HS-SH molecules have been computed from analytical expressions using multicenter multipole moments. The point charges (set of charges including both atomic and non-atomic positions) exactly reproduce both molecular and segmental multipole moments, thus constituting an accurate representation of the local anisotropy of electrostatic properties. In contrast to other known point charge models, PCM can be used to calculate not only intermolecular, but also intramolecular interactions. Comparison of these results with more accurate calculations demonstrated that PCM can correctly represent both weak and strong (intramolecular) interactions, thus indicating the merit of extending PCM to obtain improved potentials for molecular mechanics and molecular dynamics computational methods.Dedicated to Prof. Alberte PullmanPacific Northwest Laboratory is operated for the US Department of Energy by Battelle Memorial Institute under contract DE-ACO6-76RLO 1830     

Porous Organic Molecular Frameworks with Extrinsic Porosity: A Platform for Carbon Storage and Separation

The assembly of porous organic molecular frameworks (POMFs), which typically evidence common feasibility and compatibility, purification, and regeneration at practical conditions, remains a strategic challenge in modern materials science and is crucial for their favorable applications in biological, medical, and environmental realms. However, instructive knowledge of well‐organized POMF assembly by supramolecular interactions is, in general, ambiguous to date. Nevertheless, a significant advance in controlled POMF assembly has been recently achieved. This Minireview highlights these approaches, with a particular focus on the design of molecular constituents and assembly strategies. We also look beyond the field of solid‐state POMF materials into the assembly and recognition in solution, thus covering recent advances in POMFs based on material design and applications in carbon storage and separation.     

Direct Measurement of Through-Bond Effects in Molecular Multivalent Interactions

Multivalent interactions occur throughout biology, and have a number of characteristics that monovalent interactions do not. However, it remains challenging to directly measure the binding force of molecular multivalent interactions and identify the mechanism of interactions. In this study, the specific interaction between bivalent aptamer and thrombin has been measured directly and quantitatively by force-induced remnant magnetization spectroscopy to investigate the binding force and through-bond effects of the multivalent interactions. The measured differential binding forces enable through-bond effects in thrombin–aptamer complexes to be identified, where aptamer binding at exosite II produces visible effects on their binding at exosite I and vice versa. This method might be suitable for practical applications in the design of high-performance ligands.     

Self‐Assembling Proteins for Design of Anticancer Nanodrugs

Inspired by the diverse protein‐based structures and materials in organisms, proteins have been expected as promising biological components for constructing nanomaterials toward various applications. In numerous studies protein‐based nanomaterials have been constructed with the merits of abundant bioactivity and good biocompatibility. However, self‐assembly of proteins as a dominant approach in constructing anticancer nanodrugs has not been reviewed. Here, we provide a comprehensive account of the role of protein self‐assembly in fabrication, regulation, and application of anticancer nanodrugs. The supramolecular strategies, building blocks, and molecular interactions of protein self‐assembly as well as the properties, functions, and applications of the resulting nanodrugs are discussed. The applications in chemotherapy, radiotherapy, photodynamic therapy, photothermal therapy, gene therapy, and combination therapy are included. Especially, manipulation of molecular interactions for realizing cancer‐specific response and cancer theranostics are emphasized. By expounding the impact of molecular interactions on therapeutic activity, rational design of highly efficient protein‐based nanodrugs for precision anticancer therapy can be envisioned. Also, the challenges and perspectives in constructing nanodrugs based on protein self‐assembly are presented to advance clinical translation of protein‐based nanodrugs and next‐generation nanomedicine.     

Design of Agents Interacting with Immunoregulating Proteins：Potential Inhibitors of the Phenylpyruvate Tautomerase Activity Catalysed by Macrophage Migration Inhibitory Factor （MIF）

The macrophage migration inhibitory factor has been implicated in a number of immune and inflammatory processes. MIF presents particular opportunities for drug design and development with potential therapeutic applications. Drug design strategies taking into consideration of specific stereochemical and tautomeric requirements in the interaction of MIF with substrates and inhibitors allow several novel structures to be de-signed. Our investigations successfully explored the tautomeric and stereochemical aspects of new compounds of the 2-phenylpyruvic acid type, both experimentally, through synthe-sis and structural investigations and computationally, through molecular mechanics and quantum mechanics calculations.     

Excitation Energy Transfer and Exchange-Mediated Quartet State Formation in Porphyrin-Trityl Systems

Photogenerated multi-spin systems hold great promise for a range of technological applications in various fields, including molecular spintronics and artificial photosynthesis. However, the further development of these applications, via targeted design of materials with specific magnetic properties, currently still suffers from a lack of understanding of the factors influencing the underlying excited state dynamics and mechanisms on a molecular level. In particular, systematic studies, making use of different techniques to obtain complementary information, are largely missing. This work investigates the photophysics and magnetic properties of a series of three covalently-linked porphyrin-trityl compounds, bridged by a phenyl spacer. By combining the results from femtosecond transient absorption and electron paramagnetic resonance spectroscopies, we determine the efficiencies of the competing excited state reaction pathways and characterise the magnetic properties of the individual spin states, formed by the interaction between the chromophore triplet and the stable radical. The differences observed for the three investigated compounds are rationalised in the context of available theoretical models and the implications of the results of this study for the design of a molecular system with an improved intersystem crossing efficiency are discussed.     

Design of Fluorescent Hybrid Materials Based on POSS for Sensing Applications

Polyhedral oligomeric silsesquioxane (POSS) has a nanoscale silicon core and eight organic functional groups on the surface, with sizes from 0.7 to 1.5 nm. The three-dimensional nanostructures of POSS can be used to build all types of hybrid materials with specific performance and controllable nanostructures. The applications of POSS-based fluorescent materials have spread across various fields. In particular, the employment of POSS-based fluorescent materials in sensing application can achieve high sensitivity, selectivity, and stability. As a result, POSS-based fluorescent materials are attracting increasing attention due to their fascinating vistas, including unique structural features, easy fabrication, and tunable optical properties by molecular design. Here, we summarize the current available POSS-based fluorescent materials from design to sensing applications. In the design section, we introduce synthetic strategies and structures of the functionalized POSS-based fluorescent materials, as well as photophysical properties. In the application section, the typical POSS-based fluorescent materials used for the detection of various target objects are summarized with selected examples to elaborate on their wide applications.     

Macroscopic Supramolecular Assembly and Its Applications

Macroscopic supramolecular assembly (MSA) has been a recent progress in supramolecular chemistry.MSA mainly focuses on studies of the building blocks with a size beyond ten micrometers and the non-covalent interactions between these interactive building blocks to form ordered structures.MSA is essential to realize the concept of"self-assembly at all scales" by bridging most supramolecular researches at molecular level and at macroscopic scale.This review summaries the development of MSA,the basic design principle and related strategies to achieve MSA and potential applications.Correspondingly,we try to elucidate the correlations and differences between "macroscopic assembly" and MSA based on intermolecular interactions;the design principle and the underlying assembly mechanism of MSA are proposed to understand the reported MSA behaviors;to demonstrate further applications of MSA,we introduce some methods to improve the ordered degree of the assembled structures from the point of precise assembly and thus envision some possible fields for the use of MSA.     

Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge density approach

A molecular multipole expansion treatment (up to hexadecapole) is examined for its accuracy in describing hydrogen-bond electrostatic interactions, with particular reference to explaining the differences between blue-shifted C-H...O and red-shifted O-H...O bonds. In interactions of H2O and CH4 with point charges at hydrogen-bonding distances, we find that the molecular multipole treatment not only fails to reproduce ab initio energies but also forces on OH or CH bonds, and therefore cannot properly account for the electrostatic component of the interaction. A treatment based on a molecule's permanent charge density and its derivatives and the charge density and its derivatives induced by an external multipole distribution is in full accord with ab initio results, as shown by application to models of the H2O-H2O and CH4-FH systems. Such a charge density approach provides a fundamental basis for understanding the importance of interaction forces in initiating structural change and thereby altering molecular properties.