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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 (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.

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.

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.

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[nb]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., First scaffolding approach to obtain tubular-shaped contorted aromatic architectures.

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. O...

A simple model has been developed for predicting the regioselectivity of arynes using orbital electronegativity. Based on this model, the nucleophile attacks the terminus possessing lower orbital electronegativity.

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.

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.

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 (MeFnHm) 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 MeFnH1 and MeFnH2 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 fi...

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.

The regioselectivity of nucleophilic addition to substituted arynes was predicted using frontier molecular orbital contribution analysis. This model indicates that the percentage of the LUMO on the reacting terminus of the aryne is responsible for the observed regioselectivity; the nucleophile attacks the carbon possessing higher contribution of the LUMO.

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 (

The reassembling of a simple connected graph G = (V,E) is an abstraction of a problem arising in earlier studies of network analysis. Its simplest formulation is in two steps: (1) We cut every edge of G into two halves, thus obtaining a collection of n=|V| one-vertex components. (2) We splice the two halves of every edge together, not of all the edges at once, but in some ordering \Theta of the edges that minimizes two measures that depend on the edge-boundary degrees of assembled components. The edge-boundary degree of a component A (subset of V) is the number of edges in G with one endpoint in A and one endpoint in V-A. We call the maximum edge-boundary degree encountered during the reassembling process the alpha-measure of the reassembling, and the sum of all edge-boundary degrees is its beta-measure. The alpha-optimization (resp. beta-optimization) of the reassembling of G is to determine an order \Theta for splicing the edges that minimizes its alpha-measure (resp. beta-measure). There are different forms of reassembling. We consider only cases satisfying the condition that if the an edge between disjoint components A and B is spliced, then all the edges between A and B are spliced at the same time. In this report, we examine the particular case of linear reassembling, which requires that the next edge to be spliced must be adjacent to an already spliced edge. We delay other forms of reassembling to follow-up reports. We prove that alpha-optimization of linear reassembling and minimum-cutwidth linear arrangment (CutWidth) are polynomially reducible to each other, and that beta-optimization of linear reassembling and minimum-cost linear arrangement (MinArr) are polynomially reducible to each other.

The intrinsic reactivity of allopurinol oxidation is calculated using the active-site models of aldehyde oxidase and xanthine oxidase (molybdopterin cofactor, MoCo) enzymes. The effects of substrate tautomerization, deprotonation and its orientation with respect to the active-site were considered. Among several mechanistic approaches, the most favorable mechanisms are the stepwise pathways. The transition barrier for the most stable tautomer of allopurinol is around 19.83 kcal mol−1. The stepwise approaches indicate the significant role of glutamate → glutamic acid conversion in the catabolism of allopurinol. Both aldehyde oxidase (AO) and xanthine oxidase (XO) could metabolize the allopurinol to oxypurinol through the self-inhibitory mechanism. This pathway is not in accordance with the experimental results which showed the release of oxypurinol with a low half-life. This phenomenon and also the presence of experimental evidence of allopurinol interaction with cytochrome P450 and drugs which are metabolized with P450 encouraged us to investigate allopurinol oxidation using the active species of P450 enzyme, compound I (Cpd I). The P450 enzymes are responsible for the catabolism of the overwhelming majority of drugs. The detailed understanding of the P450-catalyzed mechanism could result in more precise predictions about the drug metabolism and also the drug–drug interactions. The results of this study reveal that cytochrome P450 can successfully metabolize allopurinol with both a thermodynamically and kinetically feasible mechanism. The rate-determining step of this mechanism is around 22.77 kcal mol−1. Allopurinol oxidation with P450 will lead to the release of oxypurinol, not a self-inhibitory mechanism. The outcomes of this investigation can be extended to the other purine or pyrimidine containing compounds (especially hypoxanthine) which are metabolized by this group of enzymes.

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.

Synthesizing novel electron-rich calix[n]arene derivatives to alter the electronic properties of calixarene-based materials has been one of the long-standing interests. Herein, two new electron-rich calix[n]arenes (n = 4 and 8) with different sizes were synthesized by acid-catalyzed condensation reaction of 1,3,5-tripropoxybenzene and paraformaldehyde. Both derivatives were fully characterized with 1H and 13C NMR, mass spectrometry and X-ray crystallography. Furthermore, their electrochemical properties and oxidized product (cation radicals) have also been investigated.

The electronic features of anti-tumor agent, temozolomide, and its degradation products (MTIC and metabolite AIC) have been traced by means of UV absorption spectroscopy in vacuo and aqueous media. For comparison, electronic spectra of related structures and drugs (e.g., dacarbazine) were also investigated. These investigations were carried out using time-dependent density functional theory (TD-DFT) method while the conductor like screening model (COSMO) were applied for the inclusion of solvent effects in electronic spectra. From functional benchmarking, two methods; B3LYP and O3LYP were selected among several other methods with 6-311+G(2d,p) basis set aiming to get the best results in accord with the experimental values. An assessment of the obtained spectra has shown that O3LYP functional gives a mean absolute error (MAE) from experimental absorption peaks of 4.3 nm compared to the 7.2 nm MAE value at B3LYP level in aqueous media. Furthermore, since the structural and tautomeric conformers affect the electronic spectra, conformational preferences have been analyzed in temozolomide, dacarbazine, and their related structures. Temozolomide structure possesses two rotamers that differ in the orientation of carboxamide moiety with a small energy difference (energy difference of 1.39 kcal mol-1 in vacuo and 0.35 kcal mol-1 in aqueous media at B3LYP/6-311++G(2df,3pd). The more stable and meta-stable TMZ rotamer have shown their absorption maxima at 329-334 nm, respectively, at O3LYP level in aqueous media. Applying statistical calculation according to Boltzmann population formula at 25 °C and computed weighed mean estimates the λmax of temozolomide at 331 nm, which is in notable agreement with the experimental value (330 nm). Moreover, molecular orbital composition analysis has been conducted in order to interpret these findings. Graphical Abstract Temozolomide and dacarbazine.