Towards a Density-Based Description of Chemical Bonds and Noncovalent Interactions with Pauli Energy

Chemical bonds and noncovalent interactions are extraordinarily important concepts in chemistry and beyond. Using density-based quantities to describe them has a long history in the literature, yet none can satisfactorily describe the entire spectrum of interactions from strong chemical bonds to weak van der Waals forces. In this work, employing Pauli energy as the theoretical foundation, we fill in that knowledge gap. Our results show that the newly established density-based index can describe single and multiple covalent bonds, ionic bonds, metallic bonds, and different kinds of noncovalent interactions, all with unique and readily identifiable signature shapes. Two new descriptors, NBI (nonbonding and bonding identification) index and USI (ultra-strong interaction) index, have been introduced in this work. Together with NCI (noncovalent interaction) and SCI (strong covalent interaction) indexes already available in the literature, a density-based description of both chemical bonds and noncovalent interactions is accomplished.

The improvement of biocompatibility by incorporating porphyrins into carbon dots with photodynamic effects and pH sensitivities

Photodynamic therapy (PDT) is a promising new treatment for cancer; however, the hydrophobic interactions and poor solubility in water of photosensitizers limit the use in clinic. Nanoparticles especially carbon dots have attracted the attention of the world’s scientists because of their unique properties such as good solubility and biocompatibility. In this paper, we integrated carbon dots with different porphyrins to improve the properties of porphyrins and evaluated their efficacy as PDT drugs. The spectroscopic characteristics of porphyrins nano-conjugates were studied. Singlet oxygen generation rate and the light- and dark-induced toxicity of the conjugates were studied. Our results showed that the covalent interaction between CDs and porphyrins has improved the biocompatibility. The synthesized conjugates also inherit the pH sensitivity of the carbon dots, while the conjugation also decreases the hemolysis ratio making them a promising candidate for PDT. The incorporation of carbon dots into porphyrins improved their biocompatibility by reducing toxicity.

The P3 O-Tert-Butyl-Threonine is Key to High Cellular and Antiviral Potency for Aldehyde-Based SARS-CoV-2 Main Protease Inhibitors

As an essential enzyme to SARS-CoV-2, main protease (MPro) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 sites and the N-terminal protection group, we synthesized a series of MPro inhibitors that contain 𝛽-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 site. These inhibitors have a large variation of determined IC50 values that range from 4.8 to 650 nM. The determined IC50 values reveal that relatively small side chains at both P2 and P3 sites are favorable for achieving high in vitro MPro inhibition potency, the P3 site is tolerable toward unnatural amino acids with two alkyl substituents on the 𝛼-carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of MPro bound with 16 inhibitors were determined. All structures show similar binding patterns of inhibitors at the MPro active site. A covalent interaction between the active site cysteine and a bound inhibitor was observed in all structures. In MPro, large structural variations were observed on residues N142 and Q189. All inhibitors were also characterized on their inhibition of MPro in 293T cells, which revealed their in cellulo potency that is drastically different from their in vitro enzyme inhibition potency. Inhibitors that showed high in cellulo potency all contain O-tert-butyl-threonine at the P3 site. Based on the current and a previous study, we conclude that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for peptidyl aldehyde inhibitors of MPro. This finding will be critical to the development of novel antivirals to address the current global emergency of concerning the COVID-19 pandemic.

Unveiling the Synthesis of Spirocyclic, Tricyclic and Bicyclic Triazolooxazines From Intramolecular [3+2] Azide-alkyne Cycloadditions With a Molecular Electron Density Theory Perspective

The intramolecular [3+2] cycloaddition (32CA) reactions of azido alkynes leading to spirocyclic, tricyclic and bicyclic triazolooxazines has been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) level. The Electron localization function (ELF) characterizes the azido alkynes as zwitterionic species. Analysis of the Conceptual DFT indices allows classifying the azide moiety as the electrophilic counterpart and the alkyne as the nucleophilic one. These 32CA reactions are under kinetic control with the activation free energies of 23.4 - 26.7 kcal mol-1. Along the reaction path, the pseudoradical center is created initially at C4, consistent with the Parr function analysis, however the sequence of bond formation is controlled by the energetically feasible formation of the six membered oxazine ring. The intermolecular interactions at the TSs were characterized from the Quantum Theory of Atoms in Molecules (QTAIM) study and the Non covalent interaction (NCI) gradient isosurfaces.

Hydrogen and Lithium Bonds—Lewis Acid Units Possessing Multi-Center Covalent Bonds

MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions—the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method.

Enabling Tunable Hydrophilicity of PDMS via Metal-ligand Coordinated Dynamic Networks

Polydimethylsiloxane (PDMS) has been widely used in various fields due to its appealing physical and chemical properties. However, its high hydrophobicity not only yields poor adhesion to substrates but also facilitates undesired adsorption of substances such as proteins, biofoulers, etc., which limits the performance and lifetime of PDMS. Moreover, traditional surface modification techniques are often not efficient on PDMS surfaces because of the surface reconstruction. Although new methods involving chemical modification have been developed, most of them require complicated procedures and equipment. To overcome this challenge, we incorporate metal-ligand coordination, a non-covalent interaction bearing polar functionality, into PDMS, which exposes the hydrophilicity progressively upon dynamic bond breakage and reformation. We demonstrate that the hydrophilicity of coordinated PDMS can be tailored by the choice of network structure, counter anions, and metal cations, which yield distinct network dynamics. The wetting mechanism is discussed in the context of chain reconfiguration and surface reconstruction. We also show that a properly designed metal-ligand coordinated PDMS has potential as a superior marine fouling release coating by weakening diatom attachment. Through this paper, we introduce a new concept for tuning material hydrophilicity via dynamic polar functionalities, which is applicable to a wide range of polymers.

Elimination of Interionic Hydrogen Bonding in The Imidazolium-Based Ionic Liquids

Hydrogen bonding is a phenomenon of paramount importance in room-temperature ionic liquids. The presence or absence of the hydrogen bond drastically alternates self-diffusion, shear viscosity, phase transition points, and other key properties of a pure substance. For certain applications, the presence of cation-anion hydrogen bonding is undesirable. In the present paper, we investigate perspectives of removing the hydrogen...fluorine interionic attraction in the imidazolium borates, the strongest non-covalent interaction in this type of system. Chemical modification of the tetrafluoroborate anion not only eliminates hydrogen bonding but also changes the most thermodynamically preferable orientation of the cation in the vicinity of the anion. Although the most acidic hydrogen atom of the imidazole ring remains the paramount electrophilic center of the cation, it does not engender a strong electrostatically driven coordination pattern with the properly modified anions. The reported new physical insights help compose more robust ionic liquids and tune solvation properties of the imidazolium-based RTILs.

Inhibition of XPO-1 Mediated Nuclear Export through the Michael-Acceptor Character of Chalcones

The nuclear export receptor exportin-1 (XPO1, CRM1) mediates the nuclear export of proteins that contain a leucine-rich nuclear export signal (NES) towards the cytoplasm. XPO1 is considered a relevant target in different human diseases, particularly in hematological malignancies, tumor resistance, inflammation, neurodegeneration and viral infections. Thus, its pharmacological inhibition is of significant therapeutic interest. The best inhibitors described so far (leptomycin B and SINE compounds) interact with XPO1 through a covalent interaction with Cys528 located in the NES-binding cleft of XPO1. Based on the well-established feature of chalcone derivatives to react with thiol groups via hetero-Michael addition reactions, we have synthesized two series of chalcones. Their capacity to react with thiol groups was tested by incubation with GSH to afford the hetero-Michael adducts that evolved backwards to the initial chalcone through a retro-Michael reaction, supporting that the covalent interaction with thiols could be reversible. The chalcone derivatives were evaluated in antiproliferative assays against a panel of cancer cell lines and as XPO1 inhibitors, and a good correlation was observed with the results obtained in both assays. Moreover, no inhibition of the cargo export was observed when the two prototype chalcones 9 and 10 were tested against a XPO1-mutated Jurkat cell line (XPO1C528S), highlighting the importance of the Cys at the NES-binding cleft for inhibition. Finally, their interaction at the molecular level at the NES-binding cleft was studied by applying the computational tool CovDock.