Recognition with metallo cavitands.

We describe here the effects of metal complexation on the molecular recognition behavior of cavitands with quinoxaline walls. The nitrogen atoms of the quinoxalines are near the upper rim of the vase-like shape and treatment with Pd(II) gave 2:1 metal:cavitand derivatives. Characterization by 1H, 13C NMR spectroscopy, HR ESI-MS, and computations showed that the metals bridged adjacent quinoxaline panels and gave cavitands with C2v symmetry. Both water-soluble and organic-soluble versions were prepared and their host/guest complexes with alkanes, alcohols, acids, and diols (up to C12) were studied by 1H NMR spectroscopy. Analysis of the binding behavior indicated that the metals rigidified the walls of the receptive vase conformation and enhanced the binding of hydrophobic and even water-soluble guests, compared to related cavitands reported previously. The results demonstrated that the conformational dynamics of the cavitand were slowed by the coordination of Pd(II) and stabilized the host's complexes.

The role of electric field, peripheral chains, and magnetic effects on significant 1H upfield shifts of the encapsulated molecules in chalcogen-bonded capsules.

The chalcogen-bonded homo-cavitand and hetero-cavitand AY+AY' capsules (Y, Y' = Se, Te), as well as their encapsulated complexes with one or two guest molecules have been studied theoretically via density functional theory (DFT), while the 1H NMR spectra of the homo-cavitand encapsulated complexes (in ASe+ASe) have been measured experimentally. There is excellent agreement between theoretical and experimental spectra. In all cases, we found significant 1H upfield shifts which are more intense in the ASe+ASe cage compared to the ATe+ATe and ASe+ATe cages. The non-uniform electron distribution which gives rise to an inherent electric field and a non-zero electric dipole moment of the encapsulated complexes, the induced electric field effects, the magnetic anisotropy which is enhanced due to the polarizability of chalcogen atoms, and the peripheral chains, which are responsible for the solubility of the cages, increase the upfield shifts of 1H of the encapsulated molecules; the peripheral chains lead to an increase of the upfield shifts by up to 1.8 ppm for H of the rim and up to 1.2 ppm for the terminal H in the interior of the cage. Hence, substantial 1H upfield chemical shifts of the guests in these capsules are consequences of (i) the enhanced aromaticity of the walls of the capsules due to the polarizability of chalcogen atoms, (ii) the induced and inherent electric field effects, and (iii) the peripheral chains.

Chalcogen Bonding and Hydrophobic Effects Force Molecules into Small Spaces.

Supramolecular capsules are desirable containers for the study of molecular behavior in small spaces and offer applications in transport, catalysis, and material science. We report here the use of chalcogen bonding to form container assemblies that are stable in water. Cavitands 1-3 functionalized with 2,1,3-benzoselenadiazole walls were synthesized in good yield from resorcin[4]arenes. The solid-state single-crystal X-ray structure of 3 showed a dimeric assembly cemented together through multiple Se···N chalcogen bonds. Binding of hydrophobic and amphiphilic guests in D2O was investigated by 1H NMR methods and revealed host-guest assemblies of 1:1, 2:1, and 2:2 stoichiometries. Small guests such as n-hexane or cyclohexane assembled as 2:2 capsular complexes, larger guests like cyclohexane carboxylic acid or cyclodecane formed 1:1 cavitand complexes, and longer linear guests like n-dodecane, cyclohexane carboxylic acid anhydride, and amides created 2:1 capsular complexes. The 2:1 complex of the capsule with cyclohexane carboxylic acid anhydride was stable over 2 weeks, showing that the seam of chalcogen bonds is "waterproof". Selective uptake of cyclohexane over benzene and methyl cyclohexane over toluene was observed in aqueous solution with the capsule. Hydrophobic forces and hydrogen-bonding attractions between guest molecules such as 3-methylbutanoic acid stabilized the assemblies in the presence of the competing effects of water. The high polarizability and modest electronegativity of Se provide a capsule lining complementary to guest C-H bonds. The 2,1,3-benzoselenadiazole walls impart an unusually high magnetic anisotropy to the capsule environment, which is supported by density functional theory calculations.

Aromaticity and Chemical Bonding of Chalcogen-Bonded Capsules Featuring Enhanced Magnetic Anisotropy.

We present a theoretical study of chalcogen bonded container capsules (AX +AX ) where X=O, S, Se, and Te, and their encapsulation complexes with n-C9 H20 (n-C9 H20 @AX +AX ). Both Se and Te encapsulation complexes have significant experimental and computed binding energies, analogous to the hydrogen bonded counterparts, while the S and O capsules and their encapsulation complexes show only weak binding energies, which are attributed to different types of bonding: chalcogen S⋅⋅⋅N bonds for S-capsules and π-π stacking and weak hydrogen bonds for the O case. All AX +AX and C9 H20 @AX +AX present unusually high magnetic anisotropies in their interiors. The 1 H NMR spectra of the encapsulation complexes display the proton signals of the encapsulated n-nonane highly upfield shifted, in agreement with the available experimental data for the Se capsule. We found that different factors contribute to the observed magnetic anisotropy of the capsule's interior: for the Te capsule the most important factor is Te's large polarizability; for the O analogue the inductive effects produced by the electronegative nature of the O and N heteroatoms; and for the S and Se capsules, the polarizability of the heteroatoms combines with electric field effects.

Cavitands as Containers for α,ω-Dienes and Chaperones for Olefin Metathesis.

Described herein is the behavior of α,ω-dienes sequestered within cavitands in aqueous (D2 O) solution. Hydrophobic forces drive the dienes into the cavitands in conformations that best fill the available space. Shorter dienes (C9 and C10) bind in compressed conformations that tumble rapidly in the cavitands. Longer dienes induce capsule formation between cavitands with self-complementary hydrogen bonding sites, where the dienes exist in extended conformations. In cavitands unable to form capsules, longer dienes adopt folded structures. The wider open ends allow the synthesis of medium-sized cycloalkenes by ring-closing metathesis reactions with the Hoveyda-Grubbs-II catalyst. Yields of cycloheptene and cyclooctene were enhanced by the chaperones in water when compared with reactions of the free dienes in either aqueous media or chloroform, and even cyclononene could be prepared within the cavitand.

Exfoliation and supramolecular functionalization of graphene with an electron donor perylenediimide derivative.

The liquid exfoliation of graphite to few layered graphene sheets together with the non-covalent supramolecular functionalization of exfoliated graphene by the synthesized N,N'-di(2-ethylhexyl)-1-(N''''-methylpiperazin-N'''-yl)perylene-3,4,9,10-tetracarboxydiimide (Pip-PDI) is reported. The aromatic Pip-PDI has the ability to non-covalently interact with the exfoliated graphene sheets, stabilizing them and preventing their reassembly. On the other hand, the presence of the piperazine moiety on the bay position of the PDI core makes it an ideal electron donor, nicely coupled with the electron accepting exfoliated graphene, hence, forming a novel donor-acceptor nanoensemble, which was characterized by complementary spectroscopic and microscopy techniques. Theoretical calculations predicted the absence of a meaningful charge-separated state within the Pip-PDI/graphene ensemble, which was also proven by time-resolved fluorescence and transient absorption measurements.

Molecular logic gates based on benzo-18-crown-6 ether of styrylquinoline: a theoretical study.

In the present work, we examine the possibility of a benzo-18-crown-6 ether of styrylquinoline molecule (1) in acetonitrile solvent to act as a sensor for the Ca++ cation and as a molecular logical gate. DFT and TDDFT calculations are carried out using the M06-2X and the PBE0 functionals. The quinoline moiety is an electron donor and an H+ receptor, while the crown ether is a Ca++ receptor forming host-guest complexes with Ca++. The calculations show that there are 8 thermally stable forms, i.e., trans and cis isomers of neutral (1), protonated (1H+), complexed with Ca++ (1Ca++), and both protonated and Ca++ complexed (1H+Ca++), with different absorption and emission spectra, and which can be interconverted from one form to another. The addition of H+ and/or Ca++ to 1 results in variation of the oscillator strength of the major absorption and emission peaks as well as in significant shifts of the major absorption and emission peaks including shifting from the vis spectral area to UV and vice versa. Consequently, 1 is a candidate for a sensor for the Ca++ cation. Furthermore it is shown that 1 can act as a molecular optical switch owing to its ability to be reversibly protonated and/or Ca++ complexed with substantial accompanying differences in the spectral properties. Similarly, 1 can be used as a sensor molecular logic gate, in which using H+ and Ca++ and irradiation as input, the emission output at 500, 470, 430, and 407 nm can be utilized as output to build AND, NOR, XOR, XNOR, INHIBIT, and IMPLICATION logic gates.

Electronic structure and spectra of (Cu2O)(n)-H2O complexes.

Density functional theory calculations have been employed to determine optimized geometries for different (Cu2O)n clusters for n = 1 to 6, 12 and 18. The results show the formation of (Cu2O)n rings for n ≥ 2, while (Cu2O)n nanobarrels have been determined for n = 12 and for n = 18. Adsorption of H2O on the (Cu2O)n clusters occurs preferentially by interaction of the water O with outer Cu atoms. Absorption spectra calculated by time dependent density functional theory show that in all cases charge-transfer excitations from occupied orbitals of the (Cu2O)n cluster to a Rydberg orbital of H2O contribute to the character of the singlet excited states calculated at energies starting at about 2.6 eV, with increasing contribution found at higher excitation energies. Configuration interaction calculations on selected (Cu2O)n-H2O complexes determine charge-transfer excitations to contribute significantly to excited states lying at 4.6-6.2 eV above the ground state.

Amplified halogen bonding in a small space.

Weak, intermolecular forces are difficult to observe in solution because the molecular encounters are random, short-lived, and overwhelmed by the solvent. In confined spaces such as capsules and the active sites of enzymes or receptors, the encounters are prolonged, prearranged, and isolated from the medium. We report here the application of encapsulation techniques to directly observe halogen bonding. The small volume of the capsule amplifies the concentrations of both donor and acceptor, while the shape of the space permits their proper alignment. The extended lifetime of the encapsulation complex allows the weak interaction to be observed and characterized by conventional NMR methods under conditions in which the interaction would be negligible in bulk solvent.

Social isomers of picolines in a small space.

Encapsulation complexes permit the observation of molecules under conditions of limited motion. Inside capsules, molecular encounters are prolonged, prearranged, and protected from the medium, in contrast to the short-lived and random encounters that occur in bulk solution. Herein, the interaction of α-, ß-, and γ-picolines in a cylindrical capsule is described. Two picolines were taken up, and NMR spectra indicated dynamic combinations of various social isomers. The stabilities of the complexes are interpreted through computational methods. The shape of the space in the capsule allowed the alignment of molecules and revealed delicate, atom-to-atom interactions and attractive forces that elude observation in dilute solution. These weak forces were amplified in the isolated small space of the capsule.

Pyridinium-based tripodal chemosensor in visual sensing of AMP in water by indicator displacement assay (IDA).

A simple pyridinium-based tripodal chemosensor, 1, effectively recognizes AMP over ATP and ADP through indicator displacement assay (IDA) technique in water at pH 6.4. The good recognition of 1 is due to the better accommodation of AMP at the core of 1 as well as functional interaction involving hydrogen bonding and charge-charge interaction. The sensor 1 also recognizes intracellular AMP.

Conformations and fluorescence of encapsulated stilbene.

Absorption and emission spectra of free and encapsulated stilbene in two different capsules were calculated using the DFT and the TDDFT methodology at the B3LYP, CAM-B3LYP, M06-2X, PBE0, and ωB97X-D/6-31G(d,p) levels of theory. The present work is directed toward the theoretical interpretation of recent experimental results on control of stilbene conformation and fluorescence in capsules [Ams, M. R.; et al. Beilstein J. Org. Chem. 2009, 5, 79]. The results of the calculations are in agreement with experiment and show that fluorescence of trans-stilbene persists in the large cage while it is quenched in the small one. It is found that the geometry of trans-stilbene in the ground as well as in the first excited singlet state is unaffected by encapsulation in the large cage, and consequently the absorption and emission spectra are similarly unaffected. In the small cage, the ground state of encapsulated trans-stilbene is distorted, with the two phenyl groups twisted, while the geometry of the excited state, after relaxation, lies at the conical intersection with the ground state. Consequently, there is no emission similar to that of free trans-stilbene, and the state decays nonradiatively to the ground state.

Evaluating the performance of ReaxFF potentials for sp2 carbon systems (graphene, carbon nanotubes, fullerenes) and a new ReaxFF potential.

We study the performance of eleven reactive force fields (ReaxFF), which can be used to study sp2 carbon systems. Among them a new hybrid ReaxFF is proposed combining two others and introducing two different types of C atoms. The advantages of that potential are discussed. We analyze the behavior of ReaxFFs with respect to 1) the structural and mechanical properties of graphene, its response to strain and phonon dispersion relation; 2) the energetics of (n, 0) and (n, n) carbon nanotubes (CNTs), their mechanical properties and response to strain up to fracture; 3) the energetics of the icosahedral C60 fullerene and the 40 C40 fullerene isomers. Seven of them provide not very realistic predictions for graphene, which made us focusing on the remaining, which provide reasonable results for 1) the structure, energy and phonon band structure of graphene, 2) the energetics of CNTs versus their diameter and 3) the energy of C60 and the trend of the energy of the C40 fullerene isomers versus their pentagon adjacencies, in accordance with density functional theory (DFT) calculations and/or experimental data. Moreover, the predicted fracture strain, ultimate tensile strength and strain values of CNTs are inside the range of experimental values, although overestimated with respect to DFT. However, they underestimate the Young's modulus, overestimate the Poisson's ratio of both graphene and CNTs and they display anomalous behavior of the stress - strain and Poisson's ratio - strain curves, whose origin needs further investigation.

Self Cycloaddition of o-Naphthoquinone Nitrosomethide to (±) Spiro{naphthalene(naphthopyranofurazan)}-one Oxide: An Insight into its Formation.

2-Hydroxy-1-naphthaldehyde oxime was oxidized by AgO (or Ag2 O), in presence of N-methyl morpholine N-oxide (NMMO), to the title spiro adduct-dimer (±)-Spiro{naphthalene-1(2H),4'-(naphtho[2',1':2,3]pyrano[4,5-c]furazan)}-2-one-11'-oxide by a Diels-Alder(D-A) type self-cycloaddition, through the agency of an o-naphthoquinone nitrosomethide (o-NQM). Moreover, 2-hydroxy-8-methoxy-1-naphthaldehyde oxime was prepared and subjected to the same oxidation conditions. Its sterically guided result, 9-methoxynaphtho[1,2-d]isoxazole, was isolated, instead of the expected spiro adduct. The peri intramolecular H bonding in the oxime is considered to have a key contribution to the outcome. Geometry and energy features of the oxidant- and stereo-guided selectivity of both oxidation outcomes have been explored by DFT, perturbation theory and coupled cluster calculations. The reaction free energy of the D-A intermolecular cycloaddition is calculated at -82.0 kcal/mol, indicating its predominance over the intramolecular cyclization of ca. -37.6 kcal/mol. The cycloaddition is facilitated by NMMO through dipolar interactions and hydrogen bonding with both metal complexes and o-NQM. The 8(peri)-OMe substitution of the reactant oxime sterically impedes formation of the spiro adduct, instead it undergoes a more facile cyclodehydration to the isoxazole structure by ca. 4.9 kcal/mol.

Theoretical study of hydrogen bonding in homodimers and heterodimers of amide, boronic acid, and carboxylic acid, free and in encapsulation complexes.

The homodimers and the heterodimers of two amides, two boronic acids, and two carboxylic acids have been calculated in the gas phase and in N,N-dimethylformamide (DMF) and CCl(4) solvents using the DFT (M06-2X and M06-L) and the MP2 methods in conjunction with the 6-31G(d,p) and 6-311+G(d,p) basis sets. Furthermore, their pairwise coencapsulation was studied to examine its effect on the calculated properties of the hydrogen bonds at the ONIOM[M06-2X/6-31G(d,p);PM6], ONIOM[MP2/6-31G(d,p); PM6], and M06-2X/6-31G(d,p) levels of theory. The present work is directed toward the theoretical rationalization and interpretation of recent experimental results on hydrogen bonding in encaptulation complexes [D. Ajami et al. J. Am. Chem. Soc. 2011, 133, 9689-9691]. The calculated dimerization energy (ΔE) values range from 0.74 to 0.35 eV for the different dimers in the gas phase, with the ordering carboxylic homodimers > amide-carboxylic dimers > amide homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic homodimers. In solvents, generally smaller ΔE values are calculated with only small variations in the ordering. In the capsule, the ΔE values range between 0.67 and 0.33 eV with practically the same ordering as in the gas phase. The calculated % distributions of the encapsulated dimers, taking into account statistical factors, are in agreement with the experimental distribution, where the occurrence of boronic homodimer dominates, even though it is calculated to have the smallest ΔE.

Electronic structure and absorption spectra of supramolecular complexes of a fullerene crown ether with a π-extended TTF derivative.

The present work is a theoretical investigation on supramolecular complexes of a fullerene crown ether (A and B isomers) with a derivative of π-extended tetrathiafulvalene (T). The geometry and the electronic structure of seven different conformers of the complex of dibenzo-18-crown-6 ether of fullero-N-methylpyrrolidine with a N-benzyl-N-(4-{[9,10-bis(1,3-dithiol-2-ylidene)-9,10-dihydroanthracen-2-yl]ethynyl}benzyl)ammonium cation were determined. We calculated the complexation energies and the absorption spectra, i.e., the lowest 50 excited electronic states of the complexes have been determined at the ground state optimum geometry. All calculations were carried out employing the density functional theory (DFT) and the time-dependent DFT, using the B3LYP, CAM-B3LYP, ωB97X-D, and M06-2X functionals in conjunction with the 6-31G(d,p) basis set. Various types of van der Waals interactions are observed in the complexes. Conformer complexation energies (CE) range from 2.54 to 2.14 eV in the gas phase and from 1.75 to 1.34 eV in CHCl(3) solvent at the ωB97X-D/6-31G(d,p)//M06-2X/6-31G(d,p) level of theory. There are three major features at about 390, 330, and 290 nm in the calculated absorption spectra of all the conformers. The major peaks correspond to T→T, T→T/F (electron density in both T and the fullerene F of B) and to T→F transitions, depending on the particular conformer. Other charge transfer T→F transitions are observed close to the T→T transition, indicating the possibility of photoinduced electron transfer in all these complexes.

Theoretical investigation of the complexation of crown ethers and crown ethers of fulleropyrrolidine with (CH3)(x)NH+(4-x), x = 0-4.

The electronic and geometric structures of dibenzo-12-crown-4, dibenzo-18-crown-6, and dibenzo-24-crown-8 ethers, and dibenzo-18-crown-6 ether of fullero-N-methylpyrrolidine and their complexes with (CH(3))(x)NH+(4-x), x = 0-4 were investigated by employing density functional theory (B3LYP, M05-2X, M06-2X, MPWBIK and B2PLYP-D) in conjunction with three basis sets. Different energetic minima have been identified for all of the above molecules and complexes in the gas phase as well as in CHCl(3) solvent. We report geometries, complexation energies and some thermochemical data. For increasing values of x, the complexation energies, corrected for the basis set superposition error range from 3.29 to 0.73 eV in the gas phase and from 1.56 to 0.13 eV in the CHCl(3) solvent. In the case of the largest crown ethers, the 24-crown-8 ethers are folded around the ammonium cation so as to maximize the number of hydrogen bonds formed and present the largest complexation energies. Finally, the presence of fullero-N-methylpyrrolidine, attached to the crown ethers, does not change the complexation energies substantially.

Fluorescence properties of organic dyes: quantum chemical studies on the green/blue neutral and protonated DMA-DPH emitters in polymer matrices.

The absorption and fluorescence spectra of the green emitter DMA-DPH {1-[4-(dimethylamino)phenyl]-6-phenylhexa-1,3,5-triene} and its protonated blue-emitter form have been studied theoretically through time-dependent density functional theory (TD-DFT) and resolution-of-identity 2nd order perturbative coupled cluster (RI-CC2) calculations with basis sets up to augmented triple-ζ quality, in the gas phase and in solvents of different polarity. These systems dispersed in a polymer matrix are of interest for applications in organic light emitting diode devices (OLEDs). Calculations show that the observed absorption and emission spectra correspond to transitions between the S(0) and S(1) states, in both systems. The nature and characteristics of these transitions are discussed. Excellent agreement with experimental data is obtained, both for absorption and emission, provided that the state-specific polarized continuum model (SS-PCM) method is employed for the inclusion of the solvent.

Computational insight into the electronic structure and absorption spectra of lithium complexes of N-confused tetraphenylporphyrin.

The present work is a theoretical investigation on lithium complexes of N-confused tetraphenylporphyrins (aka inverted) employing density functional theory (DFT) and time-dependent DFT, using the B3LYP, CAM-B3LYP, and M06-2X functionals in conjunction with the 6-31G(d,p) basis set. The purpose of the present study is to calculate the electronic structure and the bonding of the complexes to explain the unusual coordination environment in which Li is found experimentally and how the Li binding affects the Q and the Soret bands. The calculations show that, unlike a typical tetrahedral Li(+) cation, this Li forms a typical bond with one N and interacts with the remaining two N atoms, and it is located in the right place to form an agostic-like interaction with the internal C atom. The reaction energy, the enthalpy for the formation of the lithium complexes of N-confused porphyrins, and the effect of solvation are also calculated. The insertion of Li into N-confused porphyrin, in the presence of tetrahydrofuran, is exothermic with a reaction energy calculated to be as high as -72.4 kcal/mol using the lithium bis(trimethylsilyl)amide reagent. Finally, there is agreement in the general shape among the vis-UV spectra determined with different functionals and the experimentally available ones. The calculated geometries are in agreement with crystallographic data, where available.

Excited-state intramolecular proton transfer in hydroxyoxime-based chemical sensors.

The electronic structure of a series of ß-hydroxy-oximes, with different aromatic cores (naphthalene, pyrene, coumarin, pyridine) between the oxime and the hydroxyl groups, has been investigated by time-dependent density functional theory (TDDFT) and of the naphthalene-based oxime, in addition, by resolution-of-identity second-order perturbative coupled cluster (RICC2) calculations with basis sets up to augmented triple-ζ quality. The particular systems have been proposed as fluorescent sensors of organophosphorus (OP) nerve agents, with enhancement of fluorescence accompanying the sensing of OP agents. It is found that the experimentally observed fluorescence quenching of the oxime sensors in their initial form can be attributed to intramolecular proton transfer upon excitation from the ß-hydroxyl group to the nitrogen atom, thus forming a weakly emitting hydroxylaminoquinoid.