DFT-optimized Structures Research Articles

Experimental, Theoretical, and In Silico Studies of Potential CDC7 Kinase Inhibitors.

In this work, we present the synthesis, solid-state characterization, and in silico studies of two pyrazole derivatives: 5-(2-methylphenoxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (I) and 5-(4-methylphenoxy)-3-methyl-1-phenyl-1H-pyrazole-4-carbaldehyde (II). The molecular crystal properties, in terms of intermolecular hydrogen bonds and other weak interactions, are analyzed using single crystal X-ray diffraction. The Hirshfeld surfaces computational method is used to quantify the intermolecular interactions, density functional theory for theoretical structural optimization, and its comparison with the experimental structure and in-silico studies using docking and molecular dynamics studies of I and II with CDC7-kinase. In addition, the quantum theory of atoms in molecules (QTAIM) approach is applied to calculate the topological properties of electron density and the Laplacian of electron density of the chemical bonds of both molecules. Compounds I and II crystallize in a monoclinic crystal system, and molecules are connected via C-H···O intermolecular hydrogen bonds. Hirshfeld surfaces analysis revealed that the H···H type intercontact contributes more toward the crystal packing. DFT-optimized structures show a perfect overlay with the experimental structures. The in silico results show that both I (-41.50 kcal/mol) and II (-44.53 kcal/mol) exhibit strong binding free energies as ligands binding to the active sites of the CDC7-kinase. The most significant contributions for ligand and protein binding in both compounds are dominated by van der Waals interactions.

Tetraarylpyrrolo[3,2-b]pyrrole-BODIPY dyad: a molecular rotor for FRET-based viscosity sensing.

With the aim to develop a FRET-based viscosity sensor, two dyad molecules, 4 and 5, comprising tetraarylpyrrolo[3,2-b]pyrrole (TAPP) (donor) and naked boron-dipyrromethene (BODIPY) dyes (acceptor), were designed. Dyads were synthesized via acid-catalyzed multicomponent reactions followed by Sonogashira coupling. In both dyads, the BODIPY and TAPP moieties are linked through phenylethynyl groups, which allow free rotation of the BODIPY dyes; that is, they can act as molecular rotors. This was supported by X-ray crystallographic and DFT-optimized structures. Spectroscopic studies also confirmed the presence of both TAPP and BODIPY dyes in dyads with no electronic interactions that are suitable for fluorescence resonance energy transfer (FRET). Very high energy transfer efficiency (ETE >99%) from the donor TAPP moiety to the acceptor BODIPY moiety on excitation at the TAPP part was observed. However, due to the non-fluorescent nature of naked BODIPY dyes, no fluorescence emission was observed from the BODIPY moiety in both dyads. With increasing solvent viscosities, emission from the BODIPY moieties increases due to the restricted rotation of the BODIPY moieties. Plotting the logarithms of the fluorescent intensity of dyad 5 and the viscosity of the solution showed a good linear correlation obeying a Förster-Hoffmann equation. Non-fluorescent dyad 5 in methanol became greenish-yellow fluorescent in a methanol/glycerol (1:1) solvent. Furthermore, with an increase in the temperature of the methanol/glycerol (1:1) system, as the viscosity decreases, the fluorescence also starts decreasing. Thus, dyad 5 is capable of sensing the viscosity of the medium via a FRET-based "Off-On" mechanism. This type of viscosity sensor with a very large pseudo-Stokes shift and increased sensitivity will be useful for advancing chemo-bio sensing and imaging applications.

A Chiral Hexa-amino Cyclotriphosphazene for Enantioselective Recognition of Small Organic Compounds.

Chiral recognition and separation studies are of paramount importance in research in view of their applications in asymmetric catalysis and substrate recognition in biological processes. The efficiencies of these processes are governed by the subtle differences in noncovalent interactions between the host and guest molecules. Hexakis(organoamino)phosphazenes are versatile building blocks for host-guest chemistry for their ability to act as both the donor and the acceptor of H-bonds. Herein, we report an enantiomeric pair of cyclotriphosphazenes [P3N3(NHR*)6], [R* = (R)-(CH(CH3)Ph)] (1-R) and [(S)-(CH(CH3)Ph)] (1-S), with chiral α-methylbenzylamino substituents. The chiral recognition capabilities of its R-enantiomer were further probed for several chiral organic compounds containing a range of functional groups. Among these, a remarkable guest selectivity (ξ) value of 2506 was observed for binol (BOL) in favor of its R-enantiomer. DFT-optimized structures of the host-guest pairs suggest that the multiple noncovalent interactions between the molecules in the two unique types of binding sites at the phosphazenes play a crucial role in the observed high binding selectivities.

DFT and experimental characterization of 1-heteroatom-substituted alkylmagnesium chlorides

In addition to exhibiting nucleophilic reactivity, some alkylmagnesium chlorides that possess a heteroatom substituent at the 1-position can exhibit carbene-like reactivity. Herein, DFT calculations and experiments were performed to study the reactivity of several 1-heteroatom-substituted alkylmagnesium chlorides. The carbene character of 1-heteroatom-substituted 2-methylpropylmagneisum chlorides was evaluated using the geometric parameters in their DFT-optimized structures and the activation energies for the 1,2-hydrogen shift estimated by DFT calculations. 1-Heteroatom-substituted alkylmagnesium chlorides were generated from 1-heteroatom-substituted alkyl p-tolyl sulfoxides and isopropylmagnesium chloride via a sulfoxide/magnesium exchange reaction, and the reactivity of these species was evaluated based on the product ratio. The results revealed that 1-amino- and 1-thioalkylmagnesium chlorides were carbanions because the reaction yielded protonated products. In contrast, 1-haloalkylmagnesium chlorides were magnesium carbenoids because the reaction yielded alkene and cyclopropane without haloalkanes. Lastly, 1-pivaloxyalkylmagnesium chloride was a hybrid between carbanions and magnesium carbenoids. The order of carbene character estimated based on the theoretical results was consistent with the experimental results.

Cyanide Addition to Diiron and Diruthenium Bis-Cyclopentadienyl Complexes with Bridging Hydrocarbyl Ligands

We conducted a joint synthetic, spectroscopic and computational study to explore the reactivity towards cyanide (from Bu4NCN) of a series of dinuclear complexes based on the M2Cp2(CO)3 scaffold (M = Fe, Ru; Cp = η5-C5H5), namely [M2Cp2(CO)2(µ-CO){µ,η1:η2-CH=C=CMe2}]BF4 (1Fe-Ru), [Ru2Cp2(CO)2(µ-CO){µ,η1:η2-C(Ph)=CHPh}]BF4 (2Ru) and [M2Cp2(CO)2(µ-CO){µ-CN(Me)(R)}]CF3SO3 (3Fe-Ru). While the reaction of 1Fe with Bu4NCN resulted in prevalent allenyl deprotonation, preliminary CO-NCMe substitution in 1Ru enabled cyanide addition to both the allenyl ligand (resulting in the formation of a h1:h2-allene derivative, 5A) and the two metal centers (affording 5B1 and 5B2). The mixture of 5B1-2 was rapidly converted into 5A in heptane solution at 100 °C, with 5A being isolated with a total yield of 60%. Following carbonyl-chloride substitution in 2Ru, CN− was incorporated as a terminal ligand upon Cl− displacement, to give the alkenyl complex 6 (84%). The reactivity of 3Fe and 3Ru is strongly influenced by both the metal element, M, and the aminocarbyne substituent, R. Thus, 7aRu was obtained with a 74% yield from cyanide attack on the carbyne in 3aRu (R = Cy, cyclohexyl), whereas the reaction involving the diiron counterpart 3aFe yielded an unclean mixture of the metastable 7aFe and the CO/CN− substitution product 8aFe. The cyano-alkylidene complexes 7aRu (R = Cy) and 7bFe (R = Me) underwent CO loss and carbene to carbyne conversion in isopropanol at 60–80 °C, giving 8aRu (48%) and 8bFe (71%), respectively. The novel compounds 5A, 5B1-2, 6 and 7aRu were characterized by IR and NMR spectroscopy, with the structure of 7aRu further elucidated by single crystal X-ray diffraction analysis. Additionally, the DFT-optimized structures of potential isomers of 5A, 5B1-2 and 6 were calculated.

Synthesis and DFT-optimized structures of hydrazonal-based compound: Biological activity and molecular docking

Distinctive quinolinyl hydrazonal-based compound was synthesized by an azo-coupling reaction of an enaminonitrile (piperidinylacrylonitrile) with the diazonium salt of 8-aminoquinoline. The synthesized compound was characterized by different spectroscopic methods and displayed distinctive solvatochromism. The possible tautomeric transformation of the arylhydrazonal was studied using DFT quantum chemical calculations revealing that the E→Z tautomerization was a spontaneous exothermic process and its equilibrium constant (Keq) was high with positive power. Thus, the Z-tautomer is more favorable than E-tautomer. This study looks at arylhydrazonal's multiple biological actions, showing its substantial promise in antibacterial, antifungal, anticancer, and enzyme inhibition applications. The arylhydrazonal exhibited concentration-dependent strong antibacterial action against Gram-positive and negative bacteria. Moreover, it showed a comparable concentration-dependent antifungal efficiency against C. albicans and A. fumigatus, and close to fluconazole's potency against A. fumigatus. The arylhydrazonal exhibits significant anticancer action, targeting skin and breast cancer cells, suggesting lesser harm to normal cells. In comparison with acetazolamide (AZA), It inhibited carbonic anhydrase isozymes IX and XII with substantial potency against CA-XII. Molecular docking investigations demonstrated the compound's interactions with proteins such 1D2S, 1AS0, 4WW8, and 5Fl4, revealing different binding energies, RMSD values, and stable configurations via hydrogen bonding and π-H stacking interactions. These results highlight the compound's potential as a therapeutic agent in a variety of clinical applications, calling for more study into its development and clinical usage.

The synthesis of highly nonplanar oxidovanadium(IV) porphyrins as robust catalysts for oxidative bromination of phenols in aqueous medium

Two new complexes, oxidovanadium(IV) 2,3,5,10,12,13,15,20-octaphenyl-7,8,17,18-tetrabromoporphyrin V(IV)O(OPP)Br4 (2), and oxidovanadium(IV) 2,3,5,10,12,13,15,20-octaphenyl-7,8,17,18-tetrachloroporphyrin V(IV)O(OPP)Cl4 (3) starting from oxidovanadium(IV) 2,3,5,10,12,13,15,20-octaphenylporphyrin V(IV)O(OPP) (1) have been prepared in good yields and characterized by various spectroscopic techniques. The single-crystal and DFT-optimized structures of these porphyrins showed a highly nonplanar saddle-shape conformation of the porphyrin macrocycle. In the cyclic voltammograms, the first ring oxidation potential and the first ring reduction potential of V(IV)O(OPP)Br4 (2) and V(IV)O(OPP)Cl4 (3) showed anodic shift as compared to V(IV)O(OPP) (1), indicating the electron-deficient nature of both the porphyrins. The oxidation state of vanadium in the synthesized complexes as +4 was confirmed by EPR spectroscopy, and these porphyrins exhibited axially compressed [Formula: see text] configuration. These porphyrins were utilized as catalysts for the oxidative bromination of thymol and other phenol derivatives with excellent conversion ([Formula: see text] 99.9%), good selectivity, and high TOF value (86869 h[Formula: see text].

Isomeric Benzenediol-Linked Organophosphonates as a Handy Reusable Emitting Platform: Diversity in Polyamine Vapor Detection.

This work introduces metal/column-free facile quantitative access to conformationally twisted catechol-linked organophosphonate (CAP) as a blue-emitting solid that could reversibly detect only 1,3-diaminopropane (DAP) and 1,2-ethylenediamine (EDA) vapors, belonging to industrially and pharmaceutically abundant crucial diamines. In CAP, two adjacent hydroxy groups in a benzene ring facilitate selective diamine-dihydroxy (amine-phenol type) interactions in the solid phase, leading to a quenched emission with selectively smaller aliphatic PAs, that is, DAP and EDA. The disparity was noticed with an isomeric resorcinol-linked emitter (RAP), detecting various polyamine vapors with superior sensitivity. A one-carbon-away placed hydroxy group in RAP can only generate a monoamine-hydroxy complex, not diamine-dihydroxy. The more acidic nature of resorcinol would prefer ionizing the amines and, consequently, creating amine/hydroxy interactions. More systematic investigations reveal an exciting role of amine-hydroxy realization for the catechol analog in the solid phase with a syn-anti conformation for CAP. Unlike CAP, RAP's available crystal void space creates considerable room in which to come closer and facilitates amine-phenol interactions. The role of phosphonates in the selective detection of PAs is also examined. Observed outcomes are substantiated by FT-IR, single-crystal X-ray diffraction, SEM, XPS, and mass spectroscopic studies. The proposed amine-hydroxy interactions are further supported by DFT-optimized molecular structures.

On Some Origins of Tautomeric Preferences in Neutral Creatinine in Vacuo: Search for Analogies and Differences in Cyclic Azoles and Azines

In order to look for the origins of tautomeric preferences in neutral creatinine in vacuo, we examined prototropic conversions for model azoles, namely mono-hydroxy and mono-amino imidazoles, and also for their selected 1-methyl derivatives. All possible isomeric forms of creatinine and model compounds, resulting from intramolecular proton transfer (prototropy), conformational isomerism about –OH, and configurational isomerism about =NH, were studied in the gas phase (model of non-polar environment) by means of quantum-chemical methods. Because the bond-length alternation is a consequence of the resonance phenomenon, it was measured for all DFT-optimized structures by means of the harmonic oscillator model of electron delocalization (HOMED) index. Important HOMED analogies were discussed for investigated azoles and compared with those for previously studied cyclic azines, including pyrimidine nucleic acid bases. The internal effects were taken into account, and the stabilities of the investigated tautomers-rotamers were analyzed. Significant conclusions on the favored factors that can dictate the tautomeric preferences in creatinine were derived.

Molecular two-point recognition of fructosyl valine and fructosyl glycyl histidine in water by fluorescent Zn(II)-terpyridine complexes bearing boronic acids.

Selective recognition of fructosyl amino acids in water by arylboronic acid-based receptors is a central field of modern supramolecular chemistry that impacts biological and medicinal chemistry. Fructosyl valine (FV) and fructosyl glycyl histidine (FGH) occur as N-terminal moieties of human glycated hemoglobin; therefore, the molecular design of biomimetic receptors is an attractive, but very challenging goal. Herein, we report three novel cationic Zn-terpyridine complexes bearing a fluorescent N-quinolinium nucleus covalently linked to three different isomers of strongly acidified phenylboronic acids (ortho-, 2Zn; meta-, 3Zn and para-, 4Zn) for the optical recognition of FV, FGH and comparative analytes (D-fructose, Gly, Val and His) in pure water at physiological pH. The complexes were designed to act as fluorescent receptors using a cooperative action of boric acid and a metal chelate. Complex 3Zn was found to display the most acidic -B(OH)2 group (pKa = 6.98) and exceptionally tight affinity for FV (K = 1.43 × 105 M-1) with a strong quenching analytical response in the micromolar concentration range. The addition of fructose and the other amino acids only induced moderate optical changes. On the basis of several spectroscopic tools (1H, 11B NMR, UV-Vis, and fluorescence titrations), ESI mass spectrometry, X-ray crystal structure, and DFT calculations, the interaction mode between 3Zn and FV is proposed in a 1 : 1 model through a cooperative two-point recognition involving a sp3 boronate-diol esterification with simultaneous coordination bonding of the carboxylate group of Val to the Zn atom. Fluorescence quenching is attributed to a static complexation photoinduced electron transfer mechanism as evidenced by lifetime experiments. The addition of FGH to 3Zn notably enhanced its emission intensity with micromolar affinity, but with a lower apparent binding constant than that observed for FV. FGH interacts with 3Zn through boronate-diol complexation and coordination of the imidazole ring of His. DFT-optimized structures of complexes 3Zn-FV and 3Zn-FGH show a picture of binding which shows that the Zn-complex has a suitable (B⋯Zn) distance to the two-point recognition with these analytes. Molecular recognition of fructosyl amino acids by transition-metal-based receptors has not been explored until now.

Synthesis and Characterization of Iron Bispyridine Bisdicyanamide, Fe[C5H5N]2[N(CN)2

Fe[C5H5N]2[N(CN)2]2 (1) was synthesized from a reaction of stoichiometric amounts of NaN(CN)2 and FeCl2·4H2O in a methanol/pyridine solution. Single-crystal and powder diffraction show that 1 crystallizes in the monoclinic space group I2/m (no. 12), different from Mn[C5H5N]2[N(CN)2]2 (P21/c, no. 14) due to tilted pyridine rings, with a = 7.453(7) Å, b = 13.167(13) Å, c = 8.522(6) Å, β = 114.98(6)° and Z = 2. ATR-IR, AAS, and CHN measurements confirm the presence of dicyanamide and pyridine. Thermogravimetric analysis shows that π-stacking interactions of the pyridine rings play an important role in structural stabilization. Based on DFT-optimized structures, a chemical bonding analysis was performed using a local-orbital framework by projection from a plane-wave basis. The resulting bond orders and atomic charges are in good agreement with the expectations based on the structure analysis. SQUID magnetic susceptibility measurements show a high-spin state FeII compound with predominantly antiferromagnetic exchange interactions at lower temperatures.

Synthesis and Photophysical Properties of Dihetero[8]circulenes

Oxidation of dihydroxyhetero[7]helicenes gave dihetero[8]circulenes via the concomitant C-C coupling and dehydrative furan formation. The pristine dihetero[8]circulenes were synthesized in four steps and characterized for the first time. X-ray crystal structures and DFT-optimized structures revealed the distorted saddle-like structures, and the degree of the distortion was found to be correlated with the photophysical properties.

Nitric Oxide Oxygenation Reactions of Cobalt-Peroxo and Cobalt-Nitrosyl Complexes.

Here, we report a comparative study of nitric oxide oxidation (NOO) reactions of CoIII-peroxo (CoIII-O22-) and Co-nitrosyl ({CoNO}8) complexes bearing the same N4-donor ligand (HMTETA) framework. In this regard, we prepared and characterized two new [(HMTETA)CoIII(O22-)]+ (2, S = 2) and [(HMTETA)Co(NO)]2+ (3, S = 1) complexes from [(HMTETA)CoII(CH3CN)2]2+ (1). Both complexes (2 and 3) are characterized by different spectroscopic measurements, including their DFT-optimized structures. Complex 2 produces CoII-nitrato [(HMTETA)CoII(NO3-)]+ (CoII-NO3-, 4) complex in the presence of NO. In contrast, when 3 reacted with a superoxide (O2•-) anion, it generated CoII-nitrito [(HMTETA)CoII(NO2-)]+ (CoII-NO2-, 5) with O2 evolution. Experiments performed using 18/16O-labeled superoxide (18O2•-/16O2•-) showed that O2 originated from the O2•- anion. Both the NOO reactions are believed to proceed via a presumed peroxynitrite (PN) intermediate. Although we did not get direct spectral evidence for the proposed PN species, the mechanistic investigation using 2,4-di-tert-butylphenol indirectly suggests the formation of a PN intermediate. Furthermore, tracking the source of the N-atom in the above NOO reactions using 15N-labeled nitrogen (15NO) revealed N-atoms in 4 (CoII-15NO3-) and 5 (CoII-15NO2-) derived from the 15NO moiety.

Using Density Functional Theory for Testing the Robustness of Mobile-Proton Molecular Dynamics Simulations on Electrosprayed Ions: Structural Implications for Gaseous Proteins.

Current experiments only provide low-resolution information on gaseous protein ions generated by electrospray ionization (ESI). Molecular dynamics (MD) simulations can yield complementary insights. Unfortunately, conventional MD does not capture the mobile nature of protons in gaseous proteins. Mobile-proton MD (MPMD) overcomes this limitation. Earlier MPMD data at 300 K indicated that protein ions generated by "native" ESI retain solution-like structures with a hydrophobic core and zwitterionic exterior [Bakhtiari, M.; Konermann, L. J. Phys. Chem. B 2019, 123, 1784-1796]. MPMD redistributes protons using electrostatic and proton affinity calculations. The robustness of this approach has never been scrutinized. Here, we close this gap by benchmarking MPMD against density functional theory (DFT) at the B3LYP/6-31G* level, which is well suited for predicting proton affinities. The computational cost of DFT necessitated the use of small peptides. The MPMD energetic ranking of proton configurations was found to be consistent with DFT single-point energies, implying that MPMD can reliably identify favorable protonation sites. Peptide MPMD runs converged to DFT-optimized structures only when applying 300-500 K temperature cycling, which was necessary to prevent trapping in local minima. Temperature cycling MPMD was then applied to gaseous protein ions. Native ubiquitin converted to slightly expanded structures with a zwitterionic core and a nonpolar exterior. Our data suggest that such inside-out protein structures are intrinsically preferred in the gas phase, and that they form in ESI experiments after moderate collisional excitation. This is in contrast to native ESI (with minimal collisional excitation, simulated by MPMD at 300 K), where kinetic trapping promotes the survival of solution-like structures. In summary, this work validates the MPMD approach for simulations on gaseous peptides and proteins.

Crystal structure of toceranib, C22H25FN4O2

The crystal structure of toceranib has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Toceranib crystallizes in space group P21/c (#14) with a = 10.6899(6), b = 24.5134(4), c = 7.8747(4) Å, β = 107.7737(13)°, V = 1965.04(3) Å3, and Z = 4. The crystal structure consists of stacks of approximately planar molecules, with N–H⋯O hydrogen bonds between the layers. The commercial reagent sample was a mixture of two or more phases with toceranib being the dominant phase. The difference between the Rietveld-refined and DFT-optimized structures is larger than usual. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Quantitative analysis of steric effects on the regioselectivity of the Larock heteroannulation reaction.

Alkylphenylacetylene derivatives were synthesized and used as reactants in the Larock heteroannulation reaction to investigate the steric influence on regioselectivity. Large alkyl groups preferentially yielded 2-alkyl-3-phenylindole products, while smaller alkyl groups provided 3-alkyl-2-phenylindole as major products. The logarithm of regioisomeric product ratios exhibited good correlations with various steric parameters. Notably, the Charton values provided the best correlation when excluding the cyclopropyl group. In addition, the Boltzmann-weighted Sterimol parameter (wSterimol) was utilized to generate a good predictive model, indicating the B1 wSterimol as the significant regiochemical determining parameter with no obvious deviation for the cyclopropyl group. Relative atomic distances within the DFT-optimized transition state structures revealed good correlations with the logarithm of regioisomeric ratios. Furthermore, the cyclopropyl adsorption complex indicated electronic contribution, explaining the peculiar behavior of this substituent in the experimental observation.

Solid-state red-emissive (cyano)vinylene heteroaromatics via Pd-catalysed C-H homocoupling.

Thiophene-based π-conjugated systems are important materials for organic electronics; thus, their synthesis is of topical interest. We report fluorescent thiophene/furan-based vinylene and cyanovinylene systems via Pd-catalysed homocoupling [Pd(OAc)2, pivalic acid, KOAc, DMAc, 140 °C]. The methodology is versatile and allows the development of a variety of π-conjugated systems without the need for pre-functionalized building units. The reaction tolerates electron-rich, electron-deficient and large π-conjugated substrates. The developed compounds absorb in the visible region (400-515 nm) and emit green to orange fluorescence in the solution state (510-600 nm). Most importantly, the compounds exhibit strong aggregation-induced emission (AIE) in the NIR region (λem = 650 nm), with quantum yields reaching up to 10%. Steric hindrance imparted by vinylene/cyanovinylene units is responsible for the strong solid-state luminescence. DFT-optimized structures reveal an apparent twist of 20-40° in the molecular backbone of the compounds, supporting the AIE behaviour of the compounds.

Giant magneto optical properties in the double perovskites Ba2BʹRuO6 (Bʹ = Er, Tm)

This study aimed to investigate new double perovskite oxides in search of new promising functional material with properties of interest for high density storage applications. The crystal structure, magnetic, electronic and magneto-optical properties of the rare-earth-based double perovskites Ba2BʹRuO6 (Bʹ = Er, Tm) were investigated through full-potential linearized augmented plane wave method within the context of density functional theory (DFT) in Wien2k code. We used generalized gradient approximation (GGA) and GGA + U approaches to calculate magneto-optical properties, including spin–orbit coupling due to 4f and 4d-electrons. The obtained DFT-optimized structures was cubic (space group: Fm = 3m), and the calculations (GGA + U) showed that the compounds Ba2ErRuO6 is semiconductor and the Ba2TmRuO6 is half-metal. The magneto-optical Kerr effect showed pronounced peaks at angles of 17.7∘ and 5.6∘ for an energy around 0.2 eV for both compounds, which could potentially have important applications in the infrared region or for blue and violet radiation.

Oligonucleotides Featuring a Covalently Mercurated 6-Phenylcarbazole Residue as High-Affinity Hybridization Probes for Thiopyrimidine-Containing Sequences.

Short oligonucleotides incorporating either 1-mercuri-6-phenylcarbazole, 8-mercuri-6-phenylcarbazole, or 1,8-dimercuri-6-phenylcarbazole C-nucleoside in the middle of the chain have been synthesized and studied for their potential as hybridization probes for sequences containing thiopyrimidine nucleobases. All of these oligonucleotides formed very stable duplexes with complementary sequences pairing the organometallic moiety with either 2- or 4-thiothymine. The isomeric monomercurated oligonucleotides were also able to discriminate between 2- and 4-thiothymine based on the different melting temperatures of the respective duplexes. DFT-optimized structures of the most stable mononuclear HgII -mediated base pairs featured a coordinated covalent bond between HgII and either S2 or S4 and a hydrogen bond between the carbazole nitrogen and N3. The dinuclear HgII -mediated base pairs, in turn, were geometrically very similar to the one previously reported to form between 1,8-dimercuri-6-phenylcarbazole and thymine and had one HgII ion coordinated to a thio and the other one to an oxo substituent.

Anion Recognition by Benzoxaborole.

The binding types (H-bonding or coordinate) and stability constants for complexes of 11 mono- and di-anions with benzoxaborole (1) were determined by 1H and 11B NMR titrations in DMSO or MeCN. Compared to phenylboronic acid (PBA), 1 is a stronger Lewis acid and a poorer H-bond donor with only one B-OH group, which is expected therefore to recognize anions mostly through the coordinate bonding. This is the case however only with F-, HPO42-, and PhPO32- anions, which are coordinately bonded to 1, and partially with SO42-, which forms only the H-bonded complex with PBA, but both H-bonded and coordinate complexes with 1. The majority of tested anions (AcO-, PhPO3H-, (PhO)2PO2-, Cl-, and Br-) form H-bonded complexes with both 1 and PBA, whereas H2PO4- changes the binding mode from coordinate for PBA to H-bonded for 1. The preferable binding type for each anion is confirmed by calculations of DFT-optimized structures of the anion complexes of 1. The preferable binding type can be rationalized considering the effects of the steric hindrance, more significant for the coordinate bonding, and of increased anion basicity, which is favorable for both binding types, but enhances the strength of coordinate bonding more significantly than the strength of H-bonding.