Theoretical study on the complexes of benzene with isoelectronic nitrogen-containing heterocycles

Novel conjugated microporous polymers for efficient tetracycline adsorption: insights from theoretical investigations

This paper presents a detailed theoretical understanding of the noncovalent interactions between antibiotics tetracycline and conjugated microporous polymer (CMP), which is important to understand the recent experimental finding of efficient removal of antibiotics by CMP materials. We show that the co-work of π-π and H-π interactions determines the final equilibrium structures, when a tetracycline molecule spontaneously adsorbs to the surface or within the pores of the CMP network at physisorption distances. The binding energies for tetracycline/CMP systems are calculated to be -0.31 ∼ -1.15 eV, demonstrating the reliability of the adsorption. The electronic structures of CMP nanostructures remain basically undamaged upon the tetracycline adsorption. The replacement of benzothiadiazole unit with S and N heteroatoms to the phenyl moiety in the linker effectively enhanced the molecular polarity of CMP molecule and increases the interaction area between tetracycline and CMP network, consequently enhancing the average binding energies notably. Our calculations provide useful theoretical guidance for design of novel carbon-based porous adsorbents with good adsorption performance to remove residual tetracycline and other antibiotics in water.

Design of novel conjugated microporous polymers for efficient adsorptive desulfurization of small aromatic sulfur molecules

This paper presents a computational study of the adsorptive desulfurization of small aromatic sulfur compounds by conjugated microporous polymers (CMPs). The density-functional tight-binding method augmented with an R^-6 dispersion correction is employed to investigate the physisorption binding mechanism and electronic properties of the CMP-aromatic sulfur complexes. We show that the widely extended π conjugation in the CMP skeletons is favorable for the non-covalent adsorption of aromatic thiophene and dibenzothiophene via π-π, H-π, and S-π interactions. The average binding energies are calculated to be -6.2 ∼ -15.2 kcal/mol for CMP- thiophene/dibenzothiophene systems. For the dibenzothiophene molecule with larger size and more extended conjugation, it binds more than twice stronger to CMP than the thiophene molecule. We show that the replacement of quinoline unit to the phenylene group in the network linker effectively enhances the average binding capacities by around 0.8-1.8 kcal/mol. Our calculations theoretically demonstrate that CMPs materials are kind of promising candidates for the adsorptive desulfurization of small aromatic sulfur compounds. This paper provides useful theoretical guidance for design of novel carbon-based adsorbents for adsorptive desulfurization.

Crystal engineering of a rectangular coordination network to enable xylenes selectivity over ethylbenzene

Separation of the C8 aromatic isomers, p-xylene (PX), m-xylene (MX), o-xylene (OX) and ethylbenzene (EB), is relevant thanks to their widespread application as chemical feedstocks but challenging because of their similar boiling points and close molecular dimensions. Physisorptive separation could offer an energy-efficient solution to this challenge but sorbents which exhibit strong selectivity for one of the isomers remain a largely unmet challenge despite recent reports of OX or PX selective sorbents with high uptake capacity. For example, the square lattice, sql, topology coordination network [Co(bipy)2(NCS)2] n (sql-1-Co-NCS) exhibits the rare combination of high OX selectivity and high uptake capacity. Herein we report that a crystal engineering approach enabled isolation of the mixed-linker sql coordination network [Co(bipy)(bptz)(NCS)2] n (sql-1,3-Co-NCS, bipy = 4,4'-bipyridine, bptz = 4,4'-bis(4-pyridyl)tetrazine) and study of its C8 vapour and liquid sorption properties. sql-1,3-Co-NCS was found to exhibit high adsorption capacity from liquid xylenes (∼37 wt%) and is to our knowledge the first sorbent to exhibit high selectivity for each of xylene isomer over EB (S OX/EB, S MX/EB, S PX/EB > 5). Insights into the performance of sql-1,3-Co-NCS are gained from structural studies which reveal stacking interactions between electron-deficient bptz linkers and the respective xylenes. sql-1,3-Co-NCS is the first N-donor mixed-linker sql coordination network studied for its gas/vapour sorption properties and represents a large and diverse class of understudied coordination networks.

Chemical sensing with 2D materials

During the last decade, two-dimensional materials (2DMs) have attracted great attention due to their unique chemical and physical properties, which make them appealing platforms for diverse applications in sensing of gas, metal ions as well as relevant chemical entities.

Crystal structure of 2,9-dibromo-1,10-phenanthroline, C12H6Br2N2

C12H6Br2N2, orthorhombic, Pna21 (no. 33), a = 19.6816(9) Å, b = 4.6554(2) Å, c = 11.8795(6) Å, V = 1088.47(9) Å3, Z = 4, R gt(F) = 0.043, wR ref(F 2) = 0.107, T = 293 K.

An insight into Csp–H⋯π hydrogen bonds and stability of complexes formed by acetylene and its substituted derivatives with benzene and borazine

Theoretical calculations at the MP2/aug-cc-pVDZ level are used to investigate the C_sp–H⋯π interactions of C₂HX (X = H, F, Cl, Br, CH₃, NH₂) with C₆H₆ and B₃N₃H₆ molecules.

Theoretical study of the physisorption of organic molecules on conjugated microporous polymers: the critical role of skeleton structures on binding strength

By enlarging the size (area) in the linker or adding substituent group in the node, the binding energy between CMPs and adsorbates will increase significantly, which demonstrates the critical role of skeleton structures on binding strength.

The expanded genetic alphabet

All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on alternative hydrogen bonding, and two based on hydrophobic and packing forces. All three of these UBPs are replicated and transcribed with remarkable efficiency and fidelity, and the latter two thus demonstrate that hydrogen bonding is not unique in its ability to underlie the storage and retrieval of genetic information. This Review highlights these recent developments as well as the applications enabled by the UBPs, including the expansion of the evolution process to include new functionality and the creation of semi-synthetic life that stores increased information.

Fluorescence Quenching Nanoprobes Dedicated to In Vivo Photoacoustic Imaging and High-Efficient Tumor Therapy in Deep-Seated Tissue

Photoacoustic imaging (PAI) and photoacoustic (PA) therapy have promising applications for treating tumors. It is known that the utilization of high-absorption-coefficient probes can selectively enhance the PAI target contrast and PA tumor therapy efficiency in deep-seated tissue. Here, the design of a probe with the highest availability of optical-thermo conversion by using graphene oxide (GO) and dyes via π-π stacking interactions is reported. The GO serves as a base material for loading dyes and quenching dye fluorescence via fluorescence resonance energy transfer (FRET), with the one purpose of maximum of PA efficiency. Experiments verify that the designed fluorescence quenching nanoprobes can produce stronger PA signals than the sum of the separate signals generated in the dye and the GO. Potential applications of the fluorescence quenching nanoprobes are demonstrated, dedicating to enhance PA contrast of targets in deep-seated tissues and tumors in living mice. PA therapy efficiency both in vitro and in vivo by using the fluorescence quenching nanoprobes is found to be higher than with the commonly used PA therapy agents. Taken together, quenching dye fluorescence via FRET will provide a valid means for developing high-efficiency PA probes. Fluorescence quenching nanoprobes are likely to become a promising candidate for deep-seated tumor imaging and therapy.

The propargylbenzene dimer: C–H⋯π assisted π–π stacking

The infrared spectrum of a size-selected propargylbenzene dimer suggests the formation of a π-stacked dimer.

On the origin of the substantial stabilisation of the electron-donor 1,3-dithiole-2-thione-4-carboxyclic acid···I2 and DABCO···I2 complexes

The stabilisation energies of the crystal structures of 1,3-dithiole-2-thione-4-carboxyclic acid···I2 and DABCO···I2 complexes determined by the CCSD(T)/CBS method are very large and exceed 8 and 15 kcal mol(-1), respectively. The DFT-D method (B97-D3/def2-QZVP) strongly overestimates these stabilisation energies, which support the well-known fact that the DFT-D method is not very applicable to the study of charge-transfer complexes. On the other hand, the M06-2X/def2-QZVP method provides surprisingly reliable energies. A DFT-SAPT analysis has shown that a substantial stabilisation of these complexes arises from the charge-transfer energy included in the induction energy and that the respective induction energy is much larger than that of other non-covalently bound complexes. The total stabilisation energies of the complexes mentioned as well as of those where iodine has been replaced by lighter halogens (Br2 and Cl2) or by hetero systems (IF, ICH3, N2) correlate well with the magnitude of the σ-hole (Vs,max value) as well as with the LUMO energy. The nature of the stabilisation of all complexes between both electron donors and X2 (X = I, Br, Cl, N) systems is explained by the magnitude of the σ-hole but surprisingly also by the values of the electric quadrupole moment of these systems. Evidently, the nature of the stabilisation of halogen-bonded complexes between electron donors and systems where the first non-zero electric multipole moment is the quadrupole moment can be explained not only by the recently introduced concept of the σ-hole but also by the classical concept of electric quadrupole moments.

Effect of acceptor heteroatoms on π-hydrogen bonding interactions: a study of indole···thiophene heterodimer in a supersonic jet

Resonant two photon ionization (R2PI), IR-UV, and UV-UV double resonance spectroscopic techniques combined with quantum chemistry calculations have been used to determine the structure of indole···thiophene dimer observed in a supersonic jet. With the help of combined experimental and theoretical IR spectra it has been found that the observed dimer has a N-H···π hydrogen bonded slanted T-shaped structure. The present study demonstrates the effect of heteroatoms present in the acceptors on the strength of the π-hydrogen bonding interactions. It was concluded by Sherrill and co-workers from their theoretical study of benzene···pyridine dimer that aromatic rings containing heteroatoms are poorest π-hydrogen bond acceptors [E. G. Hohenstein and C. D. Sherrill, J. Phys. Chem. A 113, 878 (2009)]. But the current spectroscopic investigation exhibits that five membered aromatic heterocycles are favorable π-hydrogen bond acceptors. In this study, it has also been shown that thiophene is a better π-hydrogen bond acceptor than furan. The present work has immense biological significance as indole is the chromophore of tryptophan residue in the proteins and thiophene derivatives have potential therapeutic applications. Thus, understanding the binding motif between indole and thiophene in the heterodimer studied in this work may help in designing efficient drugs.

Efficient stacking on protein amide fragments

The less polar π-surface of protein amide groups is exposed in many receptor binding sites, either as part of the backbone or in Gln/Asn side chains. Using quantum chemical calculations and Protein Data Bank (PDB) searches on model systems, we investigate the energetics and geometric preferences for the stacking on amide groups of a large number of heteroarenes that are relevant to medicinal chemistry. From this study, we discern that the stacking energy of an aromatic ligand substituent can be improved by: 1) orienting the fragment dipole vector such that it is aligned in an antiparallel fashion with the dipole of the interacting protein amide group, 2) increasing its dipole moment, and 3) decreasing its π-electron density. These guidelines should be helpful to more rationally exploit this interaction type in future structure-based drug design.

JACOB: a dynamic database for computational chemistry benchmarking

JACOB (just a collection of benchmarks) is a database that contains four diverse benchmark studies, which in-turn included 72 data sets, with a total of 122,356 individual results. The database is constructed upon a dynamic web framework that allows users to retrieve data from the database via predefined categories. Additional flexibility is made available via user-defined text-based queries. Requested sets of results are then automatically presented as bar graphs, with parameters of the graphs being controllable via the URL. JACOB is currently available at www.wallerlab.org/jacob.

Exploring the structure determinants of pyrazinone derivatives as PDE5 3HC8 inhibitors: an in silico analysis

Phosphodiesterase type 5 (PDE5) inhibitors are clinically indicated for the treatment of erectile dysfunction, pulmonary hypertension and various other diseases. In this work, both ligand- and receptor-based three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were carried out using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques on 122 pyrazinone derivatives as PDE inhibitors. The resultant optimum 3D-QSAR model exhibits a proper predictive ability as indicated by the statistical results of Q² of 0.584, R(ncv)² of 0.884 and R(pre)² of 0.817, respectively. In addition, docking analysis and molecular dynamics (MD) simulation were also applied to elucidate the probable binding modes of these inhibitors. Our main findings are: (1) Introduction of bulky, electropositive and hydrophobic substituents at 12- and 19-positions can increase the biological activities. (2) N atom at 8-position is detrimental to the inhibitor activity, and the effect of N atoms at 5- and 6-positions on compound activity is co-determined by both the hydrophobic force and the π-π stacking interaction. (3) Bulky and hydrophilic substitutions are favored at the 27-position of ring D. (4) Electronegative and hydrophilic substitutions around 5- and 6-positions increase the inhibitory activity. (5) Hydrophobic forces and π-π stacking interaction with Phe786 and Phe820 are crucial in determining the binding of pyrazinone derivatives to PDE5. (6) Bulky substitutions around ring C favors selectivity against PDE11, while bulky groups near the 21-position disfavor the selectivity. The information obtained from this work can be utilized to accurately predict the binding affinity of related analogues and also facilitate future rational designs of novel PDE5 inhibitors with improved activity and selectivity.

Nitrogen substituted phenothiazine derivatives: modelling of molecular self-assembling

The study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π–π stacking nitrogen substituted phenothiazine derivatives by applying second-order Møller-Plesset perturbation (MP2), density functional (DFT) and semiempirical theories. The conformational stability of these molecular systems is mainly given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures are compared with the results obtained by the higher level theoretical methods. Additionally, the optimal configuration of the investigated supramolecular systems and their self-assembling properties are discussed.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Predicting the binding mode of known NCp7 inhibitors to facilitate the design of novel modulators

The HIV-1 nucleocapsid protein (NCp7) is an emerging target for antiretroviral therapy. Five hits have been reported to inhibit the NCp7-viral nucleic acids interaction at micromolar concentrations. We used two computationally refined structures of NCp7 as receptors to propose a reliable binding pose for these compounds, by means of computational methods. Theoretical binding modes are in agreement with available experimental data. Results lay the foundations for a rationale development of more effective NCp7 inhibitors.

Investigation of aminopyridiopyrazinones as PDE5 inhibitors: Evaluation of modifications to the central ring system

Efforts to improve the potency and physical properties of the aminopyridiopyrazinone class of PDE5 inhibitors through modification of the core ring system are described. Five new ring systems are evaluated and features that impart improved potency and improved solubility are delineated.

Effects of heteroatoms on aromatic pi-pi interactions: benzene-pyridine and pyridine dimer

Heteroatoms are found in many noncovalent complexes which are of biological importance. The effect of heteroatoms on pi-pi interactions is assessed via highly accurate quantum chemical computations for the two simplest cases of interactions between aromatic molecules containing heteroatoms, namely, benzene-pyridine and pyridine dimer. Benchmark quality estimated coupled-cluster through perturbative triples [CCSD(T)] binding energies are computed near the complete basis set limit. Comparisons to the benzene dimer are made to determine the contributions from heteroatoms. The presence of a heteroatom reduces the spatial extent of the pi-electron cloud and polarizability of pyridine as compared to benzene. As a result, the magnitude of the dispersion, exchange, and induction interactions in benzene-pyridine and pyridine dimer is generally reduced as compared to those for the benzene dimer. Benzene-pyridine and pyridine dimer bind more strongly than the benzene dimer in several configurations, and in contrast to the benzene dimer, parallel-displaced configurations can be significantly preferred over T-shaped configurations. Hydrogens para to a heteroatom are more effective "pi-hydrogen bond" donors, but aromatic rings with heteroatoms are worse "pi-hydrogen bond" acceptors.