Molecular recognition in chemical and biological systems

Design a synthetic glucose receptor using computational intelligence approach

The synthetic glucose receptors help to develop glucose sensors and alternative insulin therapies. Designing a glucose recognition molecule in an aqueous system remains a considerable challenge. Therefore, In-silico molecular screening hypothesis is proposed to overcome the difficulties found during the modeling of a molecule. The small organic compounds from compound databases are screened for glucose receptor modeling. Thereafter, the different computational models are designed that mimic natural glucose receptors based on screened compounds. The orientation and binding of glucose molecules within the developed receptor are predicted through the molecular interaction approach. The modeled receptors and receptor-glucose complex structures are used for geometry optimization and molecular dynamics computation. The docking results reveal that ZINC82047919, ZINC238094340, and ZINC238519600 compounds-based models provide better interactions with glucose and its orientation within the receptor cavity. The molecular dynamics simulation results showed that the receptor designed using compound ZINC238094340 is unable to hold the glucose and undergo significant conformation changes during simulation process. The receptor designed from ZINC238094340 and ZINC238519600 compounds is utilized as a reference glucose binding receptor in this study. The proposed computational approach is able to develop a novel glucose receptor and other glucose relative sugar molecules.

Separating Enthalpic, Configurational, and Solvation Entropic Components in Host-Guest Binding: Application to Cucurbit[7]uril Complexes through a Full In Silico Approach via Water Nanodroplets

Cucurbiturils are a family of supramolecular hosts obtained by condensation of glycoluril and formaldehyde. Cucurbit[7]uril, CB[7], is the most prominent member of the family for its biomolecular interest, arising from its mild solubility in water and for its strong binding with a large variety of guests containing nonpolar fragments such as adamantanes and ferrocene. For instance, CB[7] encapsulates diamantane diammonium iodide with an attomolar dissociation constant, a value unmatched even in natural encapsulation processes. Computational chemistry has been extensively employed to describe the enthalpic-entropic compensation principle of the molecular recognition process of cucurbituril hosts, but the synergistic contribution of experimental data is required for accurate results to be obtained. This paper proposes the first fully theoretical model able to reconcile the calculated thermodynamics of the complexation process with the experimental data obtained by calorimetry (ITC) for cucurbit[7]uril. The model allows the isolation and estimation of all of the enthalpic and entropic contributions coming from solute and solvent alike to the whole host-guest binding event and enables the straightforward calculation of the contribution of the solvation entropy to the binding.

Halogen bonding interactions in the XC5H4N···YCF3 (X = CH3, H, Cl, CN, NO2; Y = Cl, Br, I) complexes

The noncovalent interactions between the σ-hole region outside the halogen atom and the nitrogen atom of pyridine and its para-substituted derivatives are the focus of this work. Based on the analyses of the electrostatic potentials, YCF₃ (Y = Cl, Br, I) act as halogen bond donors, XC₅H₄N (X = CH₃, H, Cl, CN, NO₂) act as halogen bond acceptors, and the binary halogen-bonded complexes XC₅H₄N···YCF₃ have been designed and investigated by B3LYP-D3/aug-cc-pVDZ calculations together with the aug-cc-pVDZ-PP basis set for iodine. When the halogen bond acceptor remains unchanged, the interactions between C₅H₅N and YCF₃ (Y = Cl, Br, I) increase with the order of Y = Cl, Br, and I. When the halogen donor ICF₃ is fixed, the halogen bonding interactions decrease along the sequence of X = CH₃, H, Cl, CN, NO₂. Therefore, the halogen bond of the CH₃C₅H₄N···ICF₃ complex is the strongest. The interactions between Lewis acid YCF₃ (Y = Cl, Br, I) and pyridine and para-substituted pyridine are closed-shell and noncovalent interactions. On the one hand, when the halogen bond acceptor XC₅H₄N is fixed, with the increase of halogen atomic number, the strength of halogen bond increases; on the other hand, when the halogen bond donor ICF₃ is fixed, as the electron-withdrawing ability of the electron-withdrawing group (X) increases, the halogen bond gradually weakens.

Thermo-responsive imprinted hydrogel with switchable sialic acid recognition for selective cancer cell isolation from blood

In this work, a sialic acid (SA)-imprinted thermo-responsive hydrogel layer was prepared for selective capture and release of cancer cells. The SA-imprinting process was performed at 37 °C using thermo-responsive functional monomer, thus generating switchable SA-recognition sites with potent SA binding at 37 °C and weak binding at a lower temperature (e.g., 25 °C). Since SA is often overexpressed at the glycan terminals of cell membrane proteins or lipids, the SA-imprinted hydrogel layer could be used for selective cancer cell recognition. Our results confirmed that the hydrogel layer could efficiently capture cancer cells from not only the culture medium but also the real blood samples. In addition, the captured cells could be non-invasively released by lowing the temperature. Considering the non-invasive processing mode, considerable capture efficiency, good cell selectivity, as well as the more stable and durable SA-imprinted sites compared to natural antibodies or receptors, this thermo-responsive hydrogel layer could be used as a promising and general platform for cell-based cancer diagnosis.

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Thermo-responsive sialic acid (SA)-imprinted hydrogel layer was prepared.

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The hydrogel layer could efficiently and selective capture cancer cells at 37 °C.

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The captured cancer cells could be released at a lower temperature (e.g., 25 °C).

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The hydrogel layer could be used for capture and release cancer cells from blood.

Weak hydrogen bonds between alkyl halides and amides: The microwave spectroscopic and theoretical study of the difluoromethane⋯formamide complex

The pure rotational spectrum of the complex of difluoromethane with formamide was investigated by means of microwave spectroscopy supplemented with theoretical calculations. The hyperfine structure arising from the ¹⁴N nuclear quadrupole coupling effect was completely resolved. The most stable isomer that displays the C_s symmetry with the ∠HCH angle of difluoromethane being bisected by the ab-plane of formamide was detected. The two moieties in the detected isomer are connected via one N-H⋯F and one bifurcated CH₂⋯O weak hydrogen bonds confirmed by the non-covalent interaction plot and natural bond orbital analyses. The distances of the NH⋯F and CH₂⋯O interactions were determined to be 2.140(14) Å and 2.749(14) Å, respectively. The NH⋯F bond angle was determined to be 150.7°. Symmetry-adapted perturbation theory analysis indicates that the electrostatic component is the largest contributor to the total attractive interaction energy of the difluoromethane⋯formamide complex.

Dynamic host-guest behavior in halogen-bonded two-dimensional molecular networks investigated by scanning tunneling microscopy at the solid/liquid interface

The fabrication of supramolecularly engineered two-dimensional (2D) networks using simple molecular building blocks is an effective means for studying host-guest chemistry at surfaces toward the potential application of such systems in nanoelectronics and molecular devices. In this study, halogen-bonded molecular networks were constructed by the combination of linear halogen-bond donor and acceptor ligands, and their 2D structures at the highly oriented pyrolytic graphite/1-phenyloctane interface were studied by scanning tunneling microscopy. The bi-component blend of the molecular building blocks possessing tetradecyloxy chains formed a lozenge structure via halogen bonding. Upon the introduction of an appropriate guest molecule (e.g., coronene) into the system, the 2D structure transformed into a hexagonal array, and the central pore of this array was occupied by the guest molecules. Remarkably, the halogen bonding of the original structure was maintained after the introduction of the guest molecule. Thus, the halogen-bonded molecular networks are applicable for assembling guest species on the substrate without the requirement of the conventional rigid molecular building blocks with C 3 symmetry.

BODIPY- and Porphyrin-Based Sensors for Recognition of Amino Acids and Their Derivatives

Molecular recognition is a specific non-covalent and frequently reversible interaction between two or more systems based on synthetically predefined character of the receptor. This phenomenon has been extensively studied over past few decades, being of particular interest to researchers due to its widespread occurrence in biological systems. In fact, a straightforward inspiration by biological systems present in living matter and based on, e.g., hydrogen bonding is easily noticeable in construction of molecular probes. A separate aspect also incorporated into the molecular recognition relies on the direct interaction between host and guest with a covalent bonding. To date, various artificial systems exhibiting molecular recognition and based on both types of interactions have been reported. Owing to their rich optoelectronic properties, chromophores constitute a broad and powerful class of receptors for a diverse range of substrates. This review focuses on BODIPY and porphyrin chromophores as probes for molecular recognition and chiral discrimination of amino acids and their derivatives.

Tetrel Bonding Interactions Involving Carbon at Work: Recent Advances in Crystal Engineering and Catalysis

The σ- and π-hole interactions are used to define attractive forces involving elements of groups 12–18 of the periodic table acting as Lewis acids and any electron rich site (Lewis base, anion, and π-system). When the electrophilic atom belongs to group 14, the resulting interaction is termed a tetrel bond. In the first part of this feature paper, tetrel bonds formed in crystalline solids involving sp3-hybridized carbon atom are described and discussed by using selected structures retrieved from the Cambridge Structural Database. The interaction is characterized by a strong directionality (close to linearity) due to the small size of the σ-hole in the C-atom opposite the covalently bonded electron withdrawing group. The second part describes the utilization of two allotropic forms of carbon (C60 and carbon nanotubes) as supramolecular catalysts based on anion–π interactions (π-hole tetrel bonding). This part emphasizes that the π-hole, which is considerably more accessible by nucleophiles than the σ-hole, can be conveniently used in supramolecular catalysis.

More Than π-π-π Stacking: Contribution of Amide-π and CH-π Interactions to Crotonyllysine Binding by the AF9 YEATS Domain

Lysine crotonylation (Kcr) is a histone post-translational modification that is implicated in numerous epigenetic pathways and diseases. Recognition of Kcr by YEATS domains has been proposed to occur through intermolecular amide-π and alkene-π interactions, but little is known about the driving force of these key interactions. Herein, we probed the recognition of lysine crotonylation and acetylation by the AF9 YEATS domain through incorporation of noncanonical Phe analogs with distinct electrostatics at two positions. We found that amide-π interactions between AF9 and acyllysines are electrostatically tunable, with electron-rich rings providing more favorable interactions. This differs from trends in amide-heteroarene interactions and provides insightful information for therapeutic design. Additionally, we report for the first time that CH-π interactions at Phe28 directly contribute to AF9's recognition of acyllysines, illuminating differences among YEATS domains, as this residue is not highly conserved but has been shown to impart selectivity for specific post-translational modification.

Lipophilicity trends upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl groups

A systematic comparison of lipophilicity modulations upon fluorination of isopropyl, cyclopropyl and 3-oxetanyl substituents, at a single carbon atom, is provided using directly comparable, and easily accessible model compounds. In addition, comparison with relevant linear chain derivatives is provided, as well as lipophilicity changes occurring upon chain extension of acyclic precursors to give cyclopropyl containing compounds. For the compounds investigated, fluorination of the isopropyl substituent led to larger lipophilicity modulation compared to fluorination of the cyclopropyl substituent.

London Dispersion and Hydrogen-Bonding Interactions in Bulky Molecules: The Case of Diadamantyl Ether Complexes

Diadamantyl ether (DAE, C20 H30 O) represents a good model to study the interplay between London dispersion and hydrogen-bond interactions. By using broadband rotational spectroscopy, an accurate experimental structure of the diadamantyl ether monomer is obtained and its aggregates with water and a variety of aliphatic alcohols of increasing size are analyzed. In the monomer, C-H⋅⋅⋅H-C London dispersion attractions between the two adamantyl subunits further stabilize its structure. Water and the alcohol partners bind to diadamantyl ether through hydrogen bonding and non-covalent Owater/alcohol ⋅⋅⋅H-CDAE and C-Halcohol ⋅⋅⋅H-CDAE interactions. Electrostatic contributions drive the stabilization of all the complexes, whereas London dispersion interactions become more pronounced with increasing size of the alcohol. Complexes with dominant dispersion contributions are significantly higher in energy and were not observed in the experiment. The results presented herein shed light on the first steps of microsolvation and aggregation of molecular complexes with London dispersion energy donor (DED) groups and the kind of interactions that control them.

Switching of Electron and Ion Conductions by Reversible H2O Sorption in n-Type Organic Semiconductors

Polar H₂O molecules generally act as trapping sites and suppress the electron mobility of n-type organic semiconductors, making chemical design of H₂O-tolerant and responsive n-type semiconductors an important step toward multifunctional electron-ion coupling devices. The introduction of effective electrostatic interactions between potassium ions (K⁺) and carboxylate (-COO^-) anions into the electron-transporting naphthalenediimide π-framework enables the design of high-performance H₂O-tolerant n-type semiconductors with a reversible H₂O adsorption-desorption ability, where the electron mobility and K⁺ ionic conductivity were coupled with the reversible H₂O sorption behavior. The reversible H₂O adsorption into the crystals enhanced the electron mobility from 0.04 to 0.28 cm² V^-1 s^-1, whereas the K⁺ ionic conductivity decreased from 3.4 × 10^-5 to 4.7 × 10^-7 S cm^-1. Because this reversible electron-ion conducting switch is responsive to H₂O sorption behavior, it is a strong candidate for H₂O gating carrier transport systems.

ReSCoSS: a flexible quantum chemistry workflow identifying relevant solution conformers of drug-like molecules

Conformational equilibria are at the heart of drug design, yet their energetic description is often hampered by the insufficient accuracy of low-cost methods. Here we present a flexible and semi-automatic workflow based on quantum chemistry, ReSCoSS, designed to identify relevant conformers and predict their equilibria across different solvent environments in the Conductor-like Screening Model for Real Solvents (COSMO-RS) framework. We demonstrate the utility and accuracy of the workflow through conformational case studies on several drug-like molecules from literature where relevant conformations are known. We further show that including ReSCoSS conformers significantly improves COSMO-RS based predictions of physicochemical properties over single-conformation approaches. ReSCoSS has found broad adoption in the in-house drug discovery and development work streams and has contributed to establishing quantum-chemistry methods as a strategic pillar in ligand discovery.

Pillar[n]MaxQ: A New High Affinity Host Family for Sequestration in Water

We report the synthesis, X-ray crystal structure, and molecular recognition properties of pillar[n]arene derivative P[6]AS, which we refer to as Pillar[6]MaxQ along with analogues P[5]AS and P[7]AS toward guests 1-18. The ultratight binding affinity of P[5]AS and P[6]AS toward quaternary (di)ammonium ions renders them prime candidates for in vitro and in vivo non-covalent bioconjugation, for imaging and delivery applications, and as in vivo sequestration agents.

π covalency in the halogen bond

Halogen bonds are a highly directional class of intermolecular interactions widely employed in chemistry and chemical biology. This linear interaction is commonly viewed to be analogous to the hydrogen bond because hydrogen bonding models also intuitively describe the σ-symmetric component of halogen bonding. The possibility of π-covalency in a halogen bond is not contemplated in any known models. Here we present evidence of π-covalency being operative in halogen bonds formed between chloride and halogenated triphenylamine-based radical cations. We reach this conclusion through computational analysis of chlorine K-edge X-ray absorption spectra recorded on these halogen bonded pairs. In light of this result, we contend that halogen bonding is better described by analogy to metal coordination bonds rather than hydrogen bonds. Our revised description of the halogen bond suggests that these interactions could be employed to influence the electronic properties of conjugated molecules in unique ways.

Kinetic Stabilities and Exchange Dynamics of Water-Soluble Bis-Formamide Caviplexes Studied Using Diffusion-Ordered NMR Spectroscopy (DOSY)

A deep cavitand binds long-chain trans,trans- and trans,cis-bis-formamide isomers in water solution giving a pair of caviplexes in a ca. 60:40 ratio. Both caviplexes display in/out guest exchange dynamics that are slow on the ¹ H NMR chemical shift timescale, but fast on the EXSY timescale. We apply diffusion-ordered NMR spectroscopy (DOSY) to characterize the caviplexes. On the diffusion timescale, the guest in/out exchange processes feature intermediate dynamics allowing the assessment of their kinetic stabilities. We found that the trans,cis-bis-formamide isomers form kinetically more stable caviplexes than the trans,trans-counterparts. We also show that the kinetic stabilities of the bis-formamide caviplexes relate well with their relative thermodynamic stabilities. Fortunately, the tuning of the DOSY parameters allowed the observation of the exchange dynamics as slow processes on the experiment timescale.

Teaching old indicators even more tricks: binding affinity measurements with the guest-displacement assay (GDA)

A simple change has important consequences: the guest-displacement assay (GDA) is introduced which allows for binding affinity determinations of supramolecular complexes with spectroscopically silent hosts and guests. GDA is complementary to indicator-displacement assay for affinity measurements with soluble components, but is superior for insoluble or for weakly binding guests.

"Anti-Electrostatic" Halogen Bonding

Halogen bonding is often described as being driven predominantly by electrostatics, and thus adducts between anionic halogen bond (XB) donors (halogen-based Lewis acids) and anions seem counterintuitive. Such "anti-electrostatic" XBs have been predicted theoretically but for organic XB donors, there are currently no experimental examples except for a few cases of self-association. Reported herein is the synthesis of two negatively charged organoiodine derivatives that form anti-electrostatic XBs with anions. Even though the electrostatic potential is universally negative across the surface of both compounds, DFT calculations indicate kinetic stabilization of their halide complexes in the gas phase and particularly in solution. Experimentally, self-association of the anionic XB donors was observed in solid-state structures, resulting in dimers, trimers, and infinite chains. In addition, co-crystals with halides were obtained, representing the first cases of halogen bonding between an organic anionic XB donor and a different anion. The bond lengths of all observed interactions are 14-21 % shorter than the sum of the van der Waals radii.

A fabrication strategy for protein sensors based on an electroactive molecularly imprinted polymer: Cases of bovine serum albumin and trypsin sensing

A high-performance molecularly imprinted sensing platform inspired by natural recognition mechanisms was fabricated to detect protein by employing a linear electro-polymerizable molecularly imprinted polymer as macromonomer. This was achieved via the combination of a biosensor fabrication with a self-assembly imprinting technique without the use of chemical labels. An amphipathic electroactive copolymer was designed as macro-monomer to maintain structural integrity of the protein template via self-assembly, resulting in generation of a 3D construction around the protein molecule to form imprinted sites. Electro-polymerization was utilized not only to anchor imprinted sites but also to enhance electron transfer. The adaptable sensing platform was based on a strengthened recognition reaction between the MIP layer and template protein after the generation of an electroactive network. Bovine serum albumin (BSA) and trypsin were used as model proteins to investigate the method's generality, which gave broad detection ranges of 10^-14-10^-5 mg mL^-1 for BSA and 10^-13-10^-8 mg mL^-1 for trypsin. These results indicate that the proposed fabrication offers an effective and versatile strategy for protein recognition.

Mechanism of biomolecular recognition of trimethyllysine by the fluorinated aromatic cage of KDM5A PHD3 finger

The understanding of biomolecular recognition of posttranslationally modified histone proteins is centrally important to the histone code hypothesis. Despite extensive binding and structural studies on the readout of histones, the molecular language by which posttranslational modifications on histone proteins are read remains poorly understood. Here we report physical-organic chemistry studies on the recognition of the positively charged trimethyllysine by the electron-rich aromatic cage containing PHD3 finger of KDM5A. The aromatic character of two tryptophan residues that solely constitute the aromatic cage of KDM5A was fine-tuned by the incorporation of fluorine substituents. Our thermodynamic analyses reveal that the wild-type and fluorinated KDM5A PHD3 fingers associate equally well with trimethyllysine. This work demonstrates that the biomolecular recognition of trimethyllysine by fluorinated aromatic cages is associated with weaker cation-π interactions that are compensated by the energetically more favourable trimethyllysine-mediated release of high-energy water molecules that occupy the aromatic cage.

Hydration of Carboxyl Groups: A Route toward Molecular Recognition?

On Earth, water plays an active role in cellular life, over several scales of distance and time. At a nanoscale, water drives macromolecular conformation through hydrophobic forces and at short times acts as a proton donor/acceptor providing charge carriers for signal transmission. At longer times and larger distances, water controls osmosis, transport, and protein mobility. Neutron diffraction experiments augmented by computer simulation, show that the three-dimensional shape of the hydration shell of carboxyl and carboxylate groups belonging to different molecules is characteristic of each molecule. Different hydration shells identify and distinguish specific sites with the same chemical structure. This experimental evidence suggests an active role of water also in controlling, modulating, and mediating chemical reactions involving carboxyl and carboxylate groups.

No, Not That Way, the Other Way: Creating Active Sites in Self-Assembled Host Molecules

This Account describes our efforts over the last decade to synthesize self-assembled metal–ligand cage complexes that display reactive functional groups on their interiors. This journey has taken us down a variety of research avenues, including studying the mechanism of reversible self-assembly, analyzing ligand self-sorting properties, post-assembly reactivity, molecular recognition, and binding studies, and finally reactivity and catalysis. Each of these individual topics are discussed here, as are the lessons learned along the way and the future research outlook. These self-assembled hosts are the closest mimics of enzymes to date, as they are capable of size- and shape-selective molecular recognition, substrate activation and turnover, as well as showing less common ‘biomimetic’ properties such as the ability to employ cofactors in reactivity, and alter the prevailing mechanism of the catalyzed reactions.

1 Introduction

2 Paddlewheels and Self-Sorting Behavior

3 First-Row Transition-Metal-Mediated Assembly: Sorting and Stereochemical Control

4 Post-Assembly Reactivity

5 Molecular Recognition and Catalysis

6 Conclusions and Outlook

Advances in Biomimetic Systems for Molecular Recognition and Biosensing

Understanding the fundamentals of natural design, structure, and function has pushed the limits of current knowledge and has enabled us to transfer knowledge from the bench to the market as a product. In particular, biomimicry―one of the crucial strategies in this respect―has allowed researchers to tackle major challenges in the disciplines of engineering, biology, physics, materials science, and medicine. It has an enormous impact on these fields with pivotal applications, which are not limited to the applications of biocompatible tooth implants, programmable drug delivery systems, biocompatible tissue scaffolds, organ-on-a-chip systems, wearable platforms, molecularly imprinted polymers (MIPs), and smart biosensors. Among them, MIPs provide a versatile strategy to imitate the procedure of molecular recognition precisely, creating structural fingerprint replicas of molecules for biorecognition studies. Owing to their affordability, easy-to-fabricate/use features, stability, specificity, and multiplexing capabilities, host-guest recognition systems have largely benefitted from the MIP strategy. This review article is structured with four major points: (i) determining the requirement of biomimetic systems and denoting multiple examples in this manner; (ii) introducing the molecular imprinting method and reviewing recent literature to elaborate the power and impact of MIPs on a variety of scientific and industrial fields; (iii) exemplifying the MIP-integrated systems, i.e., chromatographic systems, lab-on-a-chip systems, and sensor systems; and (iv) closing remarks.

Arbitrary Resolution with Two Bead Types Coarse-Grained Strategy and Applications to Protein Recognition

Molecular recognition is a fundamental step in essentially any biological process. However, the kinetic processes during association and dissociation are difficult to be efficiently sampled by direct all-atom molecular dynamics simulations because of the large spatial and temporal scales. Here we propose an arbitrary resolution with two bead types (ART) coarse-grained (CG) strategy that is adept in molecular recognition. ART is a universal user-customized CG strategy that can generate a system-specific CG force field anytime and be applied to any system with an arbitrary CG resolution according to research requirements. ART CG simulations can be very efficiently performed with implicit solvation in prevalent simulation packages and provide interfaces for any enhanced sampling method. We used three applications, HLA-HIV epitope recognition, barnase-barstar association, and trimeric TRAF2 self-assembly, to validate the feasibility of the ART CG strategy, its advantages in protein recognition, and its high performance in simulations. Regular CG simulations can successfully achieve valid protein recognitions without any prior bound structure.

Cyclophane-Sustained Ultrastable Porphyrins

We report the encapsulation of free-base and zinc porphyrins by a tricyclic cyclophane receptor with subnanomolar binding affinities in water. The high affinities are sustained by the hydrophobic effect and multiple [CH···π] interactions covering large [π···π] stacking surfaces between the substrate porphyrins and the receptor. We discovered two co-conformational isomers of the 1:1 complex, where the porphyrin is orientated differently inside the binding cavity of the receptor on account of its tricyclic nature. The photophysical properties and chemical reactivities of the encapsulated porphyrins are modulated to a considerable extent by the receptor. Improved fluorescence quantum yields, red-shifted absorptions and emissions, and nearly quantitative energy transfer processes highlight the emergent photophysical enhancements. The encapsulated porphyrins enjoy unprecedented chemical stabilities, where their D/H exchange, protonation, and solvolysis under extremely acidic conditions are completely blocked. We anticipate that the ultrahigh stabilities and improved optical properties of these encapsulated porphyrins will find applications in single-molecule materials, artificial photodevices, and biomedical appliances.

Supramolecular Energy Materials

Self-assembly is a bioinspired strategy to craft materials for renewable and clean energy technologies. In plants, the alignment and assembly of the light-harvesting protein machinery in the green leaf optimize the ability to efficiently convert light from the sun to form chemical bonds. In artificial systems, strategies based on self-assembly using noncovalent interactions offer the possibility to mimic this functional correlation among molecules to optimize photocatalysis, photovoltaics, and energy storage. One of the long-term objectives of the field described here as supramolecular energy materials is to learn how to design soft materials containing light-harvesting assemblies and catalysts to generate fuels and useful chemicals. Supramolecular energy materials also hold great potential in the design of systems for photovoltaics in which intermolecular interactions in self-assembled structures, for example, in electron donor and acceptor phases, maximize charge transport and avoid exciton recombination. Possible pathways to integrate organic and inorganic structures by templating strategies and electrodeposition to create materials relevant to energy challenges including photoconductors and supercapacitors are also described. The final topic discussed is the synthesis of hybrid perovskites in which organic molecules are used to modify both structure and functions, which may include chemical stability, photovoltaics, and light emission.

Molecular Insight into the Interaction between Camptothecin and Acyclic Cucurbit[4]urils as Efficient Nanocontainers in Comparison with Cucurbit[7]uril: Molecular Docking and Molecular Dynamics Simulation

Cucurbit[n]urils (CB[n], n = 5, 6, 7, 8, 10, 14) and their derivatives due to the hydrophobic cavities and polar carbonyl portals have been considerably explored for their potential uses as drug delivery systems. It is important to understand how these macrocyclic compounds interact with guests. Camptothecin (CPT), as a natural alkaloid, is a topoisomerase inhibitor with antitumor activity against breast, pancreas, and lung cancers. The application of this drug in cancer therapy is restricted due to its low aqueous solubility and high toxicity. Recently, the complex formation between the cucurbit[7]uril (CB[7])/acyclic cucurbit[4]uril (aCB[4]) nanocontainers and CPT have been evaluated to overcome the potential drawbacks of the related drug. Herein, using computational methods, we identified the interaction mechanism of CPT with CB[7]/aCB[4]s, which consist of benzene and naphthalene sidewalls (aCB[4]_benzene and aCB[4]_naphthalene, respectively) since the experimental approaches have not completely provided information at the molecular level. Our molecular docking and molecular dynamics (MD) simulations show that CB[7] and its two acyclic derivatives form stable inclusion complexes with CPT especially through hydrophobic interactions. We also found that aCB[4]s with the aromatic sidewalls can attach to CPT through π-π interactions. This investigation highlights aCB[4]s due to the structural properties and flexible nature as better nanocontainers for controlled release delivery of pharmaceutical agents in comparison with the CB[7] nanocontainer.

Is There a Single Ideal Parameter for Halogen-Bonding-Based Lewis Acidity?

Halogen-bond donors (halogen-based Lewis acids) have now found various applications in diverse fields of chemistry. The goal of this study was to identify a parameter obtainable from a single DFT calculation that reliably describes halogen-bonding strength (Lewis acidity). First, several DFT methods were benchmarked against the CCSD(T) CBS binding data of complexes of 17 carbon-based halogen-bond donors with chloride and ammonia as representative Lewis bases, which revealed M05-2X with a partially augmented def2-TZVP(D) basis set as the best model chemistry. The best single parameter to predict halogen-bonding strengths was the static σ-hole depth, but it still provided inaccurate predictions for a series of compounds. Thus, a more reliable parameter, Ωσ* , has been developed through the linear combination of the σ-hole depth and the σ*(C-I) energy, which was further validated against neutral, cationic, halogen- and nitrogen-based halogen-bond donors with very good performance.

Molecular Recognition and Cocrystallization of Methylated and Halogenated Fragments of Danicalipin A by Enantiopure Alleno-Acetylenic Cage Receptors

Enantiopure (P)₄- and (M)₄-configured alleno-acetylenic cage (AAC) receptors offer a highly defined interior for the complexation and structure elucidation of small molecule fragments of the stereochemically complex chlorosulfolipid danicalipin A. Solution (NMR), solid state (X-ray), and theoretical investigations of the formed host-guest complexes provide insight into the conformational preferences of 14 achiral and chiral derivatives of the danicalipin A chlorohydrin core in a confined, mostly hydrophobic environment, extending previously reported studies in polar solvents. The conserved binding mode of the guests permits deciphering the effect of functional group replacements on Gibbs binding energies ΔG. A strong contribution of conformational energies toward the binding affinities is revealed, which explains why the denser packing of larger apolar domains of the guests does not necessarily lead to higher association. Enantioselective binding of chiral guests, with energetic differences ΔΔG_293 K up to 0.7 kcal mol^-1 between diastereoisomeric complexes, is explained by hydrogen- and halogen-bonding, as well as dispersion interactions. Calorimetric studies (ITC) show that the stronger binding of one enantiomer is accompanied by an increased gain in enthalpy ΔH but at the cost of a larger entropic penalty TΔS stemming from tighter binding.

Zinc(ii), copper(ii) and cadmium(ii) complexes as fluorescent chemosensors for cations

The fluorescence chemosensing behavior of Zn(ii), Cu(ii), and Cd(ii) based complexes toward cations has been described. Cation detection via conventional mechanisms, metal-metal exchange and chemodosimetric approaches along with the importance of metal ions and the scope, significance, and challenges with regard to the detection of cations by metal complex based probes will be discussed in detail. The fundamentals of photophysical behavior and mechanisms involved in the fluorescence detection of analytes will also be described. This article provides a detailed overview of Zn(ii), Cu(ii), and Cd(ii) based complexes as fluorescent probes for cations, together with essential discussions pertaining to detection mechanisms.

Stereoselective Activity of 1-Propargyl-4-styrylpiperidine-like Analogues That Can Discriminate between Monoamine Oxidase Isoforms A and B

The resurgence of interest in monoamine oxidases (MAOs) has been fueled by recent correlations of this enzymatic activity with cardiovascular, neurological, and oncological disorders. This has promoted increased research into selective MAO-A and MAO-B inhibitors. Here, we shed light on how selective inhibition of MAO-A and MAO-B can be achieved by geometric isomers of cis- and trans-1-propargyl-4-styrylpiperidines. While the cis isomers are potent human MAO-A inhibitors, the trans analogues selectively target only the MAO-B isoform. The inhibition was studied by kinetic analysis, UV-vis spectrum measurements, and X-ray crystallography. The selective inhibition of the MAO-A and MAO-B isoforms was confirmed ex vivo in mouse brain homogenates, and additional in vivo studies in mice show the therapeutic potential of 1-propargyl-4-styrylpiperidines for central nervous system disorders. This study represents a unique case of stereoselective activity of cis/trans isomers that can discriminate between structurally related enzyme isoforms.

Smart Molecular Recognition: From Key-to-Lock Principle to Memory-Based Selectivity

The formation and decomposition of inclusion compounds with a solid-solid phase transition may be very selective to the guest molecular structure. This selectivity may function in essentially different ways than defined by the classical concept of molecular recognition, which implies the preferential binding of complementary molecules. Solid inclusion compounds may take part as an initial or/and final state in several processes of different types summarized in this review, which selectivity is boosted by cooperativity of participating molecular crystals. Some of these processes resemble switching electronic devices and can be called smart giving practically absolute molecular recognition.