Directing Molecular Weaving of Covalent Organic Frameworks and Their Dimensionality by Angular Control.

Although reticular chemistry has commonly utilized mutually embracing tetrahedral metal complexes as crossing points to generate three-dimensional molecularly woven structures, weaving in two dimensions remains largely unexplored. We report a new strategy to access 2D woven COFs by controlling the angle of the usually linear linker, resulting in the successful synthesis of a 2D woven pattern based on chain-link fence. The synthesis was accomplished by linking aldehyde-functionalized copper(I) bisphenanthroline complexes with bent 4,4'-oxydianiline building units. This results in the formation of a crystalline solid, termed COF-523-Cu, whose structure was characterized by spectroscopic techniques and electron and X-ray diffraction techniques to reveal a molecularly woven, twofold-interpenetrated chain-link fence. The present work significantly advances the concept of molecular weaving and its practice in the design of complex chemical structures.

Decarboxylative Cyclization of Proline with o-Alkynylbenzaldehyde through an Unexploited 8π-Electrocyclization: A DFT Study.

We employed density functional theory (DFT) methods to investigate the most plausible mechanism of cyclization/ring expansion of proline with o-alkynylbenzaldehyde. This one-pot reaction starts with the in situ formation of azomethine ylide, which can undergo three different reaction pathways to form the final product. Two mechanisms are based on nucleophilic addition and 4π-electrocyclization of the azomethine ylide, and our results indicate that the rate-determining step (RDS) of these two cyclizations are 40.1 and 40.2 kcal/mol, respectively. The third novel pathway relies upon 8π-electrocyclization as the key step of this reaction; interestingly, the RDS of this cyclization is ∼20.6 kcal/mol, which shows this route to be most feasible. Thus, we introduce a novel mechanism for the electrocyclization reaction of conjugated azomethine ylides that can help chemists to design and access a new series of compounds.

Synthesis of Square Planar Cu4 Clusters.

Template-assisted synthesis of well-defined polynuclear clusters remains a challenge for [M4 ] square planar topologies. Herein, we present a tetraamine scaffold R L(NH2 )4 , where L is a rigidified resorcin[4]arene, to direct the formation of C4 -symmetric R L(NH)4 Cu4 clusters with Cu-Cu distances around 2.7 Å, suggesting metal-metal direct interactions are operative since the sum of copper's van der Waals radii is 2.8 Å. DFT calculations display HOMO to HOMO-3 residing all within a 0.1 eV gap. These four orbitals display significant electron density contribution from the Cu centers suggesting a delocalized electronic structure. The one-electron oxidized [Cu4 ]+ species was probed by variable temperature X-band continuous wave-electron paramagnetic resonance (CW-EPR), which displays a multiline spectrum at room temperature. This work presents a novel synthetic strategy for [M4 ] clusters and a new platform to investigate activation of small molecules.

Conjugated Molecular Nanotubes.

Molecular compounds with permanent tubular architectures displaying radial π-conjugation are exceedingly rare. Their radial and axial delocalization presents them with unique optical and electronic properties, such as remarkable tuning of their Stokes shifts, and redox switching between global and local aromaticity. Although these tubular compounds display large internal void spaces, these attributes have not been extensively explored, thus presenting future opportunities in the development of materials. By using cutting-edge synthetic methodologies to bend aromatic surfaces, large opportunities in synthesis, property discovery, and applications are expected in new members of this family of conjugated molecular nanotubes.

Mechanism-Based Inactivation of Cytochrome P450 Enzymes: Computational Insights.

Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.

Synthesis of Spiro[chromene-imidazo[1,2-a]pyridin]-3'-imines via 6-exo-dig Cyclization Reaction.

A transition-metal-free postmodification of the Groebke-Blackburn-Bienaymé (GBB) reaction for the synthesis of spiro[chromene-imidazo[1,2-a]pyridin]-3'-imine was discovered. The unusual transformation represents the first example of activation and the reaction of the imidazole carbon atom. In this postcondensational modification, KOt-Bu acts as a base, which, after the isomerization of an alkyne moiety to allene, causes the next unique nucleophilic reaction of the imidazole carbon atom that results in spirocyclic structures. The proposed reaction mechanism was confirmed based on the DFT calculations.

Electron-Transfer-Induced Self-Assembly of a Molecular Tweezer Platform.

The design and synthesis of a new molecular tweezer (T-tmp) with electron-rich pincers are reported. The stable monocationic radicals and self-assembled dimeric radicals of this molecular tweezer platform were prepared by chemical oxidative titration. With the aid of DFT calculations, it was found that the dimeric radicals with syn-syn-syn conformer has the most stable structure, with the hole primarily delocalized between parallel stacked pyrenyl groups.

Improving Performance of the SMD Solvation Model: Bondi Radii Improve Predicted Aqueous Solvation Free Energies of Ions and pKa Values of Thiols.

Calculation of the solvation free energy of ionic molecules is the principal source of errors in the quantum chemical evaluation of pKa values using implicit polarizable continuum solvent models. One of the important parameters affecting the performance of these models is the choice of atomic radii. Here, we assess the performance of the solvation model based on density (SMD) implicit solvation model employing SMD default radii (SMD) and Bondi radii (SMD-B), a set of empirical atomic radii developed based on the crystallographic data. For a set of 112 ions (60 anions and 52 cations), the SMD-B model showed lower mean unsigned error (MUE) for predicted aqueous solvation free energies (4.0 kcal/mol for anions and 2.4 kcal/mol for cations) compared to the standard SMD model (MUE of 5.0 kcal/mol for anions and 2.9 kcal/mol for cations). In particular, usage of Bondi radii improves the aqueous solvation energies of sulfur-containing ions by >5 kcal/mol compared to the SMD default radii. Indeed, for a set of 45 thiols, the SMD-B model was found to dramatically improve the predicted pKa values, with ∼1 pKa unit mean deviation from the experimental values, compared to ∼7 pKa units mean deviation for the SMD model with the default radii. These findings highlight the importance of the choice of atomic radii on the performance of the implicit solvation models.

An Electron-Rich Calix[4]arene-Based Receptor with Unprecedented Binding Affinity for Nitric Oxide.

Calixarenes have found widespread application as building blocks for the design and synthesis of functional materials in host-guest chemistry. The ongoing desire to develop a detailed understanding of the nature of NO bonding to multichromophoric π-stacked assemblies led us to develop an electron-rich methoxy derivative of calix[4]arene (3), which we show exists as a single conformer in solution at ambient temperature. Here, we examine the redox properties of this derivative, generate its cation radical (3+. ) using robust chemical oxidants, and determine the relative efficacy of its NO binding in comparison with model calixarenes. We find that 3/3+. is a remarkable receptor for NO+ /NO, with unprecedented binding efficacy. The availability of precise experimental structures of this calixarene derivative and its NO complex, obtained by X-ray crystallography, is critically important both for developing novel functional NO biosensors, and understanding the role of stacked aromatic donors in efficient NO binding, which may have relevance to biological NO transport.

An electron-transfer induced conformational transformation: from non-cofacial "sofa" to cofacial "boat" in cyclotetraveratrylene (CTTV) and formation of charge transfer complexes.

Electro-active polychromophoric assemblies that undergo clam-like electromechanic actuation represent an important class of organic functional materials. Here, we show that the readily available cyclotetraveratrylene (CTTV) undergoes oxidation-induced folding, consistent with interconversion from a non-cofacial "sofa" conformation to a cofacial "boat" conformer. It is found that the non-cofacial "sofa" conformer of CTTV forms stable electron donor-acceptor complexes with chloranil and DDQ. Electron-transfer induced conformational transformation in CTTV provides a framework for the rational design of novel organic functional molecules.

Reversible dioxygen uptake at [Cu4] clusters.

Dioxygen binding solely through non-covalent interactions is rare. In living systems, dioxygen transport takes place via iron or copper-containing biological cofactors. Specifically, a reversible covalent interaction is established when O2 binds to the mono or polynuclear metal center. However, O2 stabilization in the absence of covalent bond formation is challenging and rarely observed. Here, we demonstrate a unique example of reversible non-covalent binding of dioxygen within the cavity of a well-defined synthetic all-Cu(i) tetracopper cluster.

Nonspherical anion sequestration by C-H hydrogen bonding.

Macrocyclic arenes laid the foundations of supramolecular chemistry and their study established the fundamentals of noncovalent interactions. Advancing their frontier, here we designed rigidified resorcin[4]arenes that serve as hosts for large nonspherical anions. In one synthetic step, we vary the host's anion affinity properties by more than seven orders of magnitude. This is possible by engineering electropositive aromatic C-H bond donors in an idealized square planar geometry embedded within the host's inner cavity. The hydrogen atom's electropositivity is tuned by introducing fluorine atoms as electron withdrawing groups. These novel macrocycles, termed fluorocages, are engineered to sequester large anions. Indeed, experimental data shows an increase in the anion association constant (K a) as the number of F atoms increase. The observed trend is rationalized by DFT calculations of Hirshfeld Charges (HCs). Most importantly, fluorocages in solution showed weak-to-medium binding affinity for large anions like [PF6]- (102< K a <104 M-1), and high affinity for [MeSO3]- (K a >106).

Radially Oriented [n]Cyclo-meta-phenylenes.

Molecular compounds with zigzag carbon nanotube geometries are exceedingly rare. Here we report the synthesis and characterization of carbon-based nanotubes with zigzag geometry, best described as radially oriented [n]cyclo-meta-phenylenes, extending the tubularene family of compounds. By the incorporation of edge-sharing benzene rings into the tubularene's radial π-surface, we have uncovered the first step to give rise to the emergence of radial orbital distribution in zigzag nanorings.

Regioselectivity in the Scholl Reaction: Mono and Double [7]Helicenes.

We employed the density functionaly theory (DFT)-predicted regioselectivity of the intramolecular Scholl reaction in phenanthrene and dibenzo[g,p]chrysene frameworks to obtain π-extended mono and double [7]helicenes, respectively. The formation of these helical structures occurs despite the buildup of a large strain energy up to 30 kcal/mol compared with their most stable isomers. The twisted and strained structures were characterized and analyzed by experimental (NMR, UV-vis, emission, electrochemistry, and single-crystal X-ray diffraction) techniques and were further supported by DFT calculations.

Tubularenes.

We report the synthesis and characterization of conjugated, conformationally rigid, and electroactive carbon-based nanotubes that we term tubularenes. These structures are constructed from a resorcin[n b]arene base. Cyclization of the conjugated aromatic nanotube is achieved in one-pot eight-fold C-C bond formation via Suzuki-Miyaura cross-coupling. DFT calculations indicate a buildup of strain energy in excess of 90 kcal mol-1. The resulting architectures contain large internal void spaces >260 Å3, are fluorescent, and able to accept up to 4 electrons. This represents the first scaffolding approach that provides conjugated nanotube architectures.

Angular ladder-type meta-phenylenes: synthesis and electronic structural analysis.

Herein, we report the synthesis of two new series of angular (all-syn) ladder-type meta-[n]phenylenes (LMP, n = 3-8). One series contains keto groups at the termini bridges, denoted angular keto (AKn), the second contains alkyl groups at all bridge sp3 carbons, denoted angular alkyl (AAn). Their electronic and structural properties were delineated by a combination of electrochemistry and spectroscopic (UV-Vis and emission) methods and further supported by DFT calculations. Interestingly, experimental and DFT data show that changing the bridging group at the termini from alkyl (AAn) to keto (AKn) gives an increase in the first reduction potentials and LUMO energies, as the π-system is extended. Also, the charge (de)localization behavior is different for these two species; while the AAn compounds stablize charge with Robin-Day class III, the AKn compounds show a clear switch from class III to class II. In comparison with the linear analogues (LKn and LAn), DFT results reveal a shape independency of the charge (de)localization mechanism in acceptor-π-acceptor series (AKn/LKn).

Redox-Induced Molecular Actuators: The Case of Oxy-Alternate Bridged Cyclotetraveratrylene.

We report a practical two-step approach for the synthesis of hybrid-bridge macrocyclic molecules that has been used to synthesize two novel oxy-alternate-bridged macrocyclic molecules, oxy-alternate cyclotetraveratrylene (O-altCTTV) and oxy-alternate cyclohexaveratrylene (O-altCHV). Electrochemistry, absorption spectroscopy, X-ray crystallography, and DFT calculations demonstrate that O-altCTTV acts as a redox-induced molecular actuator, as its switches from the open conformation in the neutral state to the closed conformation in the cation-radical state.

Highly Selective Synthesis of Pillar[ n]arene ( n = 5, 6).

An efficient and highly selective synthetic method toward the preparation of pillar[ n]arenes ( n = 5, 6) is reported, based upon a high solvent-dependent selectivity found in the condensation reaction between 1,4-dialkyloxybenzene and paraformaldehyde, involving methanesulfonic acid as catalyst. Pillar[6]arene (P6) is obtained as the major product when using chloroform as solvent, while in dichloromethane pillar[5]arene (P5) is the dominant product. Accordingly, a series of P5 and P6 have been selectively synthesized with excellent yield.

Molecular Actuators in Action: Electron-Transfer-Induced Conformation Transformation in Cofacially Arrayed Polyfluorenes.

There is much current interest in the design of molecular actuators, which undergo reversible, controlled motion in response to an external stimulus (light, heat, oxidation, etc.). Here we describe the design and synthesis of a series of cofacially arrayed polyfluorenes (MeF nH m) with varied end-capping groups, which undergo redox-controlled electromechanical actuation. Such cofacially arrayed polyfluorenes are a model molecular scaffold to investigate fundamental processes of charge and energy transfer across a π-stacked assembly, and we show with the aid of NMR and optical spectroscopies, X-ray crystallography and DFT calculations that in the neutral state the conformation of MeF nH1 and MeF nH2 is open rather than cofacial, with a conformational dependence that is highly influenced by the local environment. Upon (electro)chemical oxidation, these systems undergo a reversible transformation into a closed fully π-stacked conformation, driven by charge-resonance stabilization of the cationic charge. These findings are expected to aid the design of novel wire-like cofacially arrayed systems capable of undergo redox-controlled actuation.