Covalent Systems Research Articles

Rational design of covalent heptazine framework photocatalysts with high oxidation ability through reaction-dependent strategy

Due to structural tunability, high surface area, abundant pore structures, and abundant active sites, covalent heptazine frameworks (CHFs) constructed from heptazine and other molecular blocks are especially prominent. Here, we proposed a reaction-dependent strategy for designing two dimensional CHFs including high-throughput precursors screening, structure generation, and performance evaluation. Assuming that oxamide-like precursors can undergo the same thermal polymerization reaction as producing C6N7, seven precursors were screened from more than 109 molecules in the ZINC20 database in terms of molecular weight, number of substructures, shape index, and symmetry. Furthermore, CHF-L1 to CHF-L7 were constructed from urea and the seven precursors according to the topologically assembling scheme in thermal polymerization. The designed CHFs had band gaps ranging from 1.89 to 3.10 eV. Among them, CHF-L3 assembled structurally by urea and 1,2,4,5-tetrazine-3,6-dicarboxamide with the smallest bandgap and an oxidative potential bias of 1.38 V for oxygen evolution reaction was screened as the candidate with high oxidative ability. The negative formation energy based on the synthesis route indicated the synthetic feasibility of CHF-L3, and negative cohesive energy as well as the stable structure under ab initio molecular dynamics simulations confirmed the stability of CHF-L3. The present work is expected to provide a powerful design strategy for two-dimensional CHFs design and is broadly applicable to various computational covalent organic framework design systems and experimental studies.

ULYSSES: An Efficient and Easy to Use Semiempirical Library for C+.

We introduce ULYSSES, a user-friendly and robust C++ library for semiempirical quantum chemical calculations. In its current version, ULYSSES is equipped with a large set of different semiempirical models, most of which are based on the Neglect of Diatomic Differential Overlap (NDDO) approximation. Empirical corrections for dispersion and hydrogen bonding are available for most methods, so that higher quality is achieved in the calculation of energies of nonbonded complexes. The library is furthermore equipped with geometry optimization, as well as modules for calculating molecular properties of general interest. Ideal gas thermodynamics is available and allows single structure as well as conformer (multistructure) averaged properties to be calculated. We offer the possibility to use several vibrational partition functions according to the nature of interactions being studied: for covalent systems, the traditional harmonic oscillator approximation is available; for nonbonded complexes, we systematically extended the partition function proposed by Grimme for all thermodynamic functions. The library is also capable of running Born-Oppenheimer molecular dynamics.

EAPOTc: An integrated empirical interatomic potential optimization platform for compound solids

The extension of interatomic potentials from elemental solids to compound ones causes a bottleneck in atomistic simulations of multi-component solids such as intermetallic compounds and solid solutions. In contrast to several extensive tools released to construct elemental potentials, such as MEAMfit and ATOMICREX, very little software has been specifically designed for multi-component solids. Herein, we extend our recently proposed software EAPOTs (Empirical interAtomic POTentials for single elemental solids) to interatomic potentials of compound solids. This new software-termed as EAPOTc or the integrated Empirical interAtomic POTential optimization platform for compound solids-provides robust multi-level objective optimization strategies with various cross potential functions and extensive combinations of multiple targets such as energy, stress, force, and elasticity. Compatibility with published elemental potentials was also implemented in EAPOTc to ensure seamless combinations of different sources of elemental potentials by using the transformation invariance rules without reliability loss for the original elemental potentials. Similar to our EAPOTs code, a high-throughput (HT) scheme was designed based on automatic communication using first-principles code (e.g., VASP) to retrieve the derived properties based on energy, stress, force, and elasticity; in addition, multiple objective optimization procedures were included. The efficiency and flexibility of EAPOTc were critically validated and tested for various metallic and covalent compound systems, including HT implementation and applicability testing for extreme scenarios. Our software demonstrated several advantages, such as a concise and user-friendly graphical user interface, extensive compatibility between elemental potentials, robust optimization schemes, and a high degree of functional integration.

Sulfur in Dynamic Covalent Chemistry

AbstractSulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur‐based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

Sulfur in Dynamic Covalent Chemistry

Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.

Reinforcing DNA Supramolecular Hydrogel with Polymeric Multiple-Unit Linker

Reinforcing DNA Supramolecular Hydrogel with Polymeric Multiple-Unit Linker

Light-Induced Formation/Scission of C-N, C-O, and C-S Bonds Enables Switchable Stability/Degradability in Covalent Systems.

The manipulation of covalent bonds could be directed toward degradable, recyclable, and sustainable materials. However, there is an intrinsic conflict between properties of stability and degradability. Here we report light-controlled formation/scission of three types of covalent bonds (C-N, C-O, and C-S) through photoswitching between equilibrium and nonequilibrium states of dynamic covalent systems, achieving dual benefits of photoaddressable stability and cleavability. The photocyclization of dithienylethene fused aldehyde ring-chain tautomers turns on the reactivity, incorporating/releasing amines, alcohols, and thiols reversibly with high efficiency, respectively. Upon photocycloreversion the system is shifted to kinetically locked out-of-equilibrium form, enabling remarkable robustness of covalent assemblies. Reaction coupling allows remote and directional control of a diverse range of equilibria and further broadens the scope. Through locking and unlocking covalent linkages with light when needed, the utility is demonstrated with capture/release of bioactive molecules, modification of surfaces, and creation of polymers exhibiting tailored stability and degradability/recyclability. The versatile toolbox for photoswitchable dynamic covalent reactions to toggle matters on and off should be appealing to many endeavors.

Hybrid Atomic Orbital Basis from First Principles: Bottom-Up Mapping of Self-Energy Correction to Large Covalent Systems.

Construction of hybrid atomic orbitals is proposed as the approximate common eigenstates of finite first moment matrices. Their hybridization and orientation can be a priori tuned as per their anticipated neighborhood. Their Wannier function counterparts constructed from the Kohn-Sham (KS) single particle states constitute an orthonormal multiorbital tight binding (TB) basis resembling hybrid atomic orbitals locked to their immediate atomic neighborhood, while spanning the subspace of KS states. The proposed basis thus renders predominantly single TB parameters from first principles for each nearest neighbor bond involving no more than two orbitals irrespective of their orientation and also facilitates an easy route for the transfer of such TB parameters across isostructural systems exclusively through mapping of neighborhoods and projection of orbital charge centers. With hybridized 2s, 2p and 3s, 3p valence electrons, the spatial extent of the self-energy correction (SEC) to TB parameters in the proposed basis is found to be localized mostly within the third nearest neighborhood, thus allowing effective transfer of self-energy-corrected TB parameters from smaller reference systems to much larger target systems, with nominal additional computational cost beyond that required for explicit computation of SEC in the reference systems. The proposed approach promises inexpensive estimation of the quasi-particle structures of large covalent systems with workable accuracy.

Molecular Gears: From Solution to Surfaces.

This review highlights the major efforts devoted to the development of molecular gears over the past 40 years, from pioneering covalent bis-triptycyl systems undergoing intramolecular correlated rotation in solution, to the most recent examples of gearing systems anchored on a surface, which allow intermolecular transmission of mechanical power. Emphasis is laid on the different strategies devised progressively to control the architectures of molecular bevel and spur gears, as intramolecular systems in solution or intermolecular systems on surfaces, while aiming at increased efficiency, complexity and functionality.

Efficient Embedded Cluster Density Approximation Calculations with an Orbital-Free Treatment of Environments.

The computational cost of the Kohn-Sham density functional theory (KS-DFT), employing advanced orbital-based exchange-correlation (XC) functionals, increases quickly for large systems. To tackle this problem, we recently developed a local correlation method in the framework of KS-DFT: the embedded cluster density approximation (ECDA). The aim of ECDA is to obtain accurate electronic structures in an entire system. With ECDA, for each atom in a system, we define a cluster to enclose that atom, with the rest atoms treated as the environment. The system's electron density is then partitioned among the cluster and the environment. The cluster's XC energy density is then calculated based on its electron density using an advanced orbital-based XC functional. The system's XC energy is obtained by patching all clusters' XC energy densities in an atom-by-atom manner. In our previous formulation of ECDA, environments were treated by KS-DFT, which makes the following two tasks computationally expensive for large systems. The first task is to partition the system's electron density among a cluster and its environment. The second task is to solve the environments' Sternheimer equations for calculating the system's XC potential. In this work, we remove these two computational bottlenecks by treating the environments with the orbital-free (OF) DFT. The new method is called ECDA-envOF. The performance of ECDA-envOF is examined in two systems: ester and Cl-tetracene, for which the exact exchange (EXX) is used as the advanced XC functional. We show that ECDA-envOF gives results that are very close to the previous formulation in which the environments were treated by KS-DFT. Therefore, ECDA-envOF can be used for future large-scale simulations. Another focus of this work is to examine ECDA-envOF's performance on systems having different bond types. With ECDA-envOF, we calculate the energy curves for stretching/compressing some covalent, metallic, and ionic systems. ECDA-envOF's predictions agree well with the benchmarks by using reasonably large clusters. These examples demonstrate that ECDA-envOF is nearly a black-box local correlation method for investigating heterogeneous materials in which different bond types exist.

Covalent Organic Polymers and Frameworks for Fluorescence-Based Sensors.

Following the advancements and diversification in synthetic strategies for porous covalent materials in the literature, the materials science community started to investigate the performance of covalent organic polymers (COPs) and covalent organic frameworks (COFs) in applications that require large surface areas for interaction with other molecules, chemical stability, and insolubility. Sensorics is an area where COPs and COFs have demonstrated immense potential and achieved high levels of sensitivity and selectivity on account of their tunable structures. In this review, we focus on those covalent polymeric systems that use fluorescence spectroscopy as a method of detection. After briefly reviewing the physical basis of fluorescence-based sensors, we delve into various kinds of analytes that have been explored with COPs and COFs, namely, heavy metal ions, explosives, biological molecules, amines, pH, volatile organic compounds and solvents, iodine, enantiomers, gases, and anions. Throughout this work, we discuss the mechanisms involved in each sensing application and aim to quantify the potency of the discussed sensors by providing limits of detection and quenching constants when available. This review concludes with a summary of the surveyed literature and raises a few concerns that should be addressed in the future development of COP and COF fluorescence-based sensors.

Probing Physical Oxidation State by Resonant X-ray Emission Spectroscopy: Applications to Iron Model Complexes and Nitrogenase.

The ability of resonant X‐ray emission spectroscopy (XES) to recover physical oxidation state information, which may often be ambiguous in conventional X‐ray spectroscopy, is demonstrated. By combining Kβ XES with resonant excitation in the XAS pre‐edge region, resonant Kβ XES (or 1s3p RXES) data are obtained, which probe the 3dn+1 final‐state configuration. Comparison of the non‐resonant and resonant XES for a series of high‐spin ferrous and ferric complexes shows that oxidation state assignments that were previously unclear are now easily made. The present study spans iron tetrachlorides, iron sulfur clusters, and the MoFe protein of nitrogenase. While 1s3p RXES studies have previously been reported, to our knowledge, 1s3p RXES has not been previously utilized to resolve questions of metal valency in highly covalent systems. As such, the approach presented herein provides chemists with means to more rigorously and quantitatively address challenging electronic‐structure questions.

Probing Physical Oxidation State by Resonant X‐ray Emission Spectroscopy: Applications to Iron Model Complexes and Nitrogenase

AbstractThe ability of resonant X‐ray emission spectroscopy (XES) to recover physical oxidation state information, which may often be ambiguous in conventional X‐ray spectroscopy, is demonstrated. By combining Kβ XES with resonant excitation in the XAS pre‐edge region, resonant Kβ XES (or 1s3p RXES) data are obtained, which probe the 3dn+1 final‐state configuration. Comparison of the non‐resonant and resonant XES for a series of high‐spin ferrous and ferric complexes shows that oxidation state assignments that were previously unclear are now easily made. The present study spans iron tetrachlorides, iron sulfur clusters, and the MoFe protein of nitrogenase. While 1s3p RXES studies have previously been reported, to our knowledge, 1s3p RXES has not been previously utilized to resolve questions of metal valency in highly covalent systems. As such, the approach presented herein provides chemists with means to more rigorously and quantitatively address challenging electronic‐structure questions.

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.

A new many-body expansion scheme for atomic clusters: Application to nitrogen clusters

Although the many-body expansion (MBE) approach is widely applied to estimate the energy of large systems containing weak interactions, it is inapplicable to calculating the energies of covalent or metal clusters. In this work, we propose an interaction many-body expansion (IMBE) to calculate the energy of atomic clusters containing covalent bonds. In this approach, the energy of a system is expressed as the sum of the energy of atoms and the interaction energy between the atom and its surrounding atoms. The IMBE method is first applied to calculate the energies of nitrogen clusters, in which the interatomic interactions are truncated to four-body terms. The results show that the IMBE approach could significantly reduce the energy error for nitrogen clusters compared with the traditional MBE method. The weak size and structure dependence of the IMBE error with respect to DFT calculations indicates the IMBE method has good potential application in estimating energy of large covalent systems.

New Small-Molecule Glycoconjugates of Docetaxel and GalNAc for Targeted Delivery to Hepatocellular Carcinoma.

In this work, we have developed covalent and low molecular weight docetaxel delivery systems based on conjugation with N-acetyl-d-galactosamine and studied their properties related to hepatocellular carcinoma cells. The resulting glycoconjugates have an excellent affinity to the asialoglycoprotein receptor (ASGPR) in the nanomolar range of concentrations and a high cytotoxicity level comparable to docetaxel. Likewise, we observed the 21-75-fold increase in water solubility in comparison with parent docetaxel and prodrug lability to intracellular conditions with half-life values from 25.5 to 42 h. We also found that the trivalent conjugate possessed selective toxicity against hepatoma cells vs control cell lines (20-35 times). The absence of such selectivity in the case of monovalent conjugates indicates the effect of ligand valency. Specific ASGPR-mediated cellular uptake of conjugates was proved in vitro using fluorescent-labeled analogues. In addition, we showed an enhanced generation of reactive oxygen species in the HepG2 cells, which could be inhibited by the natural ligand of ASGPR. Overall, the obtained results highlight the potential of ASGPR-directed cytostatic taxane drugs for selective therapy of hepatocellular carcinoma.

Fe3O4/Porphyrin Covalent Organic Framework Core–Shell Nanospheres as Interfacial Catalysts for Enzymatic Esterification

A nanoscale core-shell-structured magnetic microsphere (abbreviated as Fe3O4@DhaTph-lipase), which consists of an Fe3O4 core, a porphyrin covalent organic framework DhaTph shell with loaded lipase, is reported. The obtained Fe3O4@DhaTph-lipase microsphere can be a powerful emulsifier to stabilize the water-in-n-hexane Pickering emulsion for at least one month without any demulsification under ambient conditions. Furthermore, Fe3O4@DhaTph-lipase with lipase enzyme and a large specific surface area is a droplet microreactor and displays excellent interfacial catalytic activity to promote enzymatic esterification reaction via visible light-induced photothermal conversion. On the other hand, the magnetically triggered Pickering emulsion interfacial catalyst can be recycled at least 10 times with robust performance. The potential utility of this strategy is highlighted by the fabrication of many more multifunctional covalent organic framework-based Pickering emulsion catalytic systems to promote various organic transformations in a green, smart, and facile way.

Hydrogen-Bond Catalysis of Imine Exchange in Dynamic Covalent Systems.

The reversibility of imine bonds has been exploited to great effect in the field of dynamic covalent chemistry, with applications such as preparation of functional systems, dynamic materials, molecular machines, and covalent organic frameworks. However, acid catalysis is commonly needed for efficient equilibration of imine mixtures. Herein, it is demonstrated that hydrogen bond donors such as thioureas and squaramides can catalyze the equilibration of dynamic imine systems under unprecedentedly mild conditions. Catalysis occurs in a range of solvents and in the presence of many sensitive additives, showing moderate to good rate accelerations for both imine metathesis and transimination with amines, hydrazines, and hydroxylamines. Furthermore, the catalyst proved simple to immobilize, introducing both reusability and extended control of the equilibration process.

Charge-transfer energy in iridates: A hard x-ray photoelectron spectroscopy study

We have investigated the electronic structure of iridates in the double perovskite crystal structure containing either Ir$^{4+}$ or Ir$^{5+}$ using hard x-ray photoelectron spectroscopy. The experimental valence band spectra can be well reproduced using tight binding calculations including only the Ir $5d$, O $2p$ and O $2s$ orbitals with parameters based on the downfolding of the density-functional band structure results. We found that regardless of the A and B cations, the A$_2$BIrO$_6$ iridates have essentially zero O $2p$ to Ir $5d$ charge transfer energies. Hence, double perovskite iridates turn out to be extremely covalent systems with the consequence being that the magnetic exchange interactions become very long-ranged, thereby hampering the materialization of the long-sought Kitaev physics. Nevertheless, it still would be possible to realize a spin-liquid system using the iridates with a proper tuning of the various competing exchange interactions.

Asymmetric Ring-Opening of Epoxides Catalyzed by Metal–Salen Complexes

The asymmetric ring-opening of epoxides is an important reaction in organic synthesis, since it allows for the enantioselective installation of two vicinal functional groups with specific stereochemistry within one step from a highly available starting material. An effective class of catalysts for the asymmetric ring-opening of epoxides is metal–salen complexes. This review summarizes the development of metal–salen catalyzed enantioselective desymmetrization of meso-epoxides and kinetic resolution of epoxides with various nucleophiles, including the design and application of both homogeneous- and heterogeneous epoxide-opening catalysts as well as multi-metallic covalent and supramolecular catalytic systems.