Anion Complexes with Tetrazine-Based Ligands: Formation of Strong Anion-π Interactions in Solution and in the Solid State.

Ligands L1 and L2, consisting of a tetrazine ring decorated with two morpholine pendants of different lengths, show peculiar anion-binding behaviors. In several cases, even the neutral ligands, in addition to their protonated HL(+) and H2L(2+) (L = L1 and L2) forms, bind anions such as F(-), NO3(-), PF6(-), ClO4(-), and SO4(2-) to form stable complexes in water. The crystal structures of H2L1(PF6)2·2H2O, H2L1(ClO4)2·2H2O, H2L2(NO3)2, H2L2(PF6)2·H2O, and H2L2(ClO4)2·H2O show that anion-π interactions are pivotal for the formation of these complexes, although other weak forces may contribute to their stability. Complex stability constants were determined by means of potentiometric titration in aqueous solution at 298.1 K, while dissection of the free-energy change of association (ΔG°) into its enthalpic (ΔH°) and entropic (TΔS°) components was accomplished by means of isothermal titration calorimetry measurements. Stability constants are poorly regulated by anion-ligand charge-charge attraction. Thermodynamic data show that the formation of complexes with neutral ligands, which are principally stabilized by anion-π interactions, is enthalpically favorable (-ΔG°, 11.1-17.5 kJ/mol; ΔH°, -2.3 to -0.5 kJ/mol; TΔS°, 9.0-17.0 kJ/mol), while for charged ligands, enthalpy changes are mostly unfavorable. Complexation reactions are invariably promoted by large and favorable entropic contributions. The importance of desolvation phenomena manifested by such thermodynamic data was confirmed by the hydrodynamic results obtained by means of diffusion NMR spectroscopy. In the case of L2, complexation equilibria were also studied in a 80:20 (v/v) water/ethanol mixture. In this mixed solvent of lower dielectric constant than water, the stability of anion complexes decreases, relative to water. Solvation effects, mostly involving the ligand, are thought to be responsible for this peculiar behavior.

Antiaromatic character of 16 π electron octaethylporphyrins: magnetically induced ring currents from DFT-GIMIC calculations.

The magnetically induced current density susceptibility, also called current density, has been calculated for a recently synthesized octaethylporphyrin (OEP) zinc(II) dication with formally 16 π electrons. Numerical integration of the current density passing selected chemical bonds yields the current pathway around the porphyrinoid ring and the strength of the ring current. The current strengths show that the OEP-Zn(II) dication is strongly antiaromatic, as also concluded experimentally. The calculation of the ring current pathway shows that all 24 π electrons participate in the transport of the ring current because the current splits into inner and outer branches of practically equal strengths at the four pyrrolic rings. The corresponding neutral octaethylporphyrinoid without Zn and inner hydrogens is found to be antiaromatic, sustaining a paratropic ring current along the inner pathway with 16 π electrons. The neutral OEP-Zn(II) molecule with formally 18 π electrons is found to be almost as aromatic as free-base porphyrin. However, also in this case, all 26 π electrons contribute to the ring current, as for free-base porphyrin. A comparison of calculated and measured (1)H NMR chemical shifts is presented. The current strength susceptibility under experimental conditions has been estimated by assuming a linear relation between experimental shielding constants and calculated current strengths.

Mechanism of diffusion slowdown in confined liquids.

With the aid of molecular dynamics simulation, we consider why the diffusivity of liquid becomes slower as the liquid is confined to a narrower space. The diffusion coefficient of octamethylcyclotetrasiloxane liquid confined between two mica surfaces was calculated for a range of surface separations from 64 to 23 Å. The resulting separation dependence of the diffusion coefficient can be explained by considering that the molecular diffusion is an activated process. In particular, we find that the increase in the activation energy is closely correlated with the decrease of the potential energy per molecule, from which we propose a molecular-level mechanism of this confined-induced diffusion slowdown.

Effect of fluorine substitution on the aromaticity of polycyclic hydrocarbons.

The effect of fluorine substitution on the aromaticity of polycyclic hydrocarbons (PAH) is investigated. Magnetically induced current densities, current pathways, and current strengths, which can be used to assess molecular aromaticity, are calculated using the gauge-including magnetically induced current method (GIMIC). The degree of aromaticity of the individual rings is compared to those obtained using calculated nucleus-independent chemical shifts at the ring centers (NICS(0) and NICS(0)(zz)). Calculations of explicitly integrated current strengths for selected bonds show that the aromatic character of the investigated polycyclic hydrocarbons is weakened upon fluorination. In contrast, the NICS(0) values for the fluorinated benzenes increase noteworthy upon fluorination, predicting a strong strengthening of the aromatic character of the arene rings. The integrated current strengths also yield explicit current pathways for the studied molecules. The current pathways of the investigated linear polyacenes, pyrene, anthanthrene, coronene, ovalene, and phenanthro-ovalene are not significantly affected by fluorination. NISC(0) and NICS(0)(zz) calculations provide contradictory degrees of aromaticity of the fused individual ring. Obtained NICS values do not correlate with the current strengths circling around the individual rings.

Aromatic pathways in mono- and bisphosphorous singly Möbius twisted [28] and [30]hexaphyrins.

Magnetically induced current densities and strengths of currents passing through selected bonds have been calculated for monophosphorous [28]hexaphyrin ((PO)[28]hp) and for bisphosphorous [30]hexaphyrin ((PO)(2)[30]hp) at the density functional theory level using our gauge-including magnetically induced current (GIMIC) approach. The current-density calculations yield quantitative information about electron-delocalization pathways and aromatic properties of singly Möbius twisted hexaphyrins. The calculations confirm that (PO)[28]hp sustains a strong diatropic ring current (susceptibility) of 15 nA T(-1) and can be considered aromatic, whereas (PO)(2)[30]hp is antiaromatic as it sustains a paratropic ring current of -10 nA T(-1). Numerical integration of the current density passing through selected bonds shows that the current is generally split at the pyrroles into an outer and an inner pathway. For the pyrrole with the NH moiety pointing outwards, the diatropic ring current of (PO)[28]hp takes the outer route across the NH unit, whereas for (PO)(2)[30]hp, the paratropic ring current passes through the inner C(ß)=C(ß) double bond. The main diatropic ring current of (PO)[28]hp generally prefers the outer routes at the pyrroles, whereas the paratropic ring current of (PO)(2)[30]hp prefers the inner ones. In some cases, the ring current is rather equally split along the two pathways at the pyrroles. The calculated ring-current pathways do not agree with those deduced from measured (1)H NMR chemical shifts.

Unraveling the properties of octamethylcyclotetrasiloxane under nanoscale confinement: atomistic view of the liquidlike state from molecular dynamics simulation.

We developed an atomistic model of octamethylcyclotetrasiloxane (OMCTS) liquid confined within the nanospace between two flat mica surfaces. Molecular dynamics simulation was carried out for the liquidlike state where OMCTS liquid is not frozen, while forming molecular layers parallel to the surface. With the aid of a layer by layer analysis of the intra- and interlayer microscopic structures and the dynamics, it is found that the difference in the properties of the inner layers and the bulk liquid are relatively small in spite of the clear differences in the structure. This leads to the conclusion that the layered structure itself is an appearance of the microscopic structure that already exists in the bulk liquid. The most striking difference from the bulk liquid is mainly seen in the contact layer, where characteristic molecular orientations that are not seen in the crystalline phase appeared, and the dynamics of the liquid becomes 2-3 orders of magnitude slower than that of the bulk.

Magnetically induced currents in [n]cycloparaphenylenes, n = 6-11.

We report calculations of the gauge-independent magnetically induced current densities in [n]cycloparaphenylenes ([n]CP), n = 6-11. In addition to the neutral [n]CPs, the dianion of [6]CP and the current densities of the corresponding metal complexes Li(2)[6]CP and Mg[6]CP are also investigated. By the ring current criterion, the [6]CP with 4n pi electrons has a slight antiaromatic character, while [7]CP has (4n + 2) pi electrons and is weakly aromatic with a ring current susceptibility strength that is about 25% of the ring current of benzene. The larger neutral [n]CPs, n = 8-11, do not sustain any net ring current around the nanohoop and are essentially nonaromatic. The weak paramagnetic ring current susceptibility of [6]CP flows along a 4n pi pathway on either edge of the phenylene rings. For the dianions, the ring current susceptibility strengths are 24-35 nA/T diatropic and thus the addition of two electrons induces an electron delocalization and an aromatic character of the nanohoops. The dilithium complex of [6]CP with (4n + 2) pi electrons is aromatic with a net ring current strength of 28 nA/T or 2.4 times the ring current strength of benzene, involving all 62 pi electrons in the current pathway. The (1)H NMR chemical shieldings and the nucleus-independent chemical shifts correlate with the strengths of the magnetically induced currents. The aromatic [n]cycloparaphenylenes have a quinoid structure, whereas the weakly aromatic or nonaromatic ones are benzoidic.

Conformational control of benzyl-o-carboranylbenzene derivatives and molecular encapsulation of acetone in the dynamically formed space of 1,3,5-tris(2-benzyl-o-carboran-1-yl)benzene.

A 1,3,5-substituted benzene platform has been widely used in the fields of supramolecular chemistry and molecular recognition. Here, we show that 1,3,5-tris(2-benzyl-o-carboran-1-yl)benzene 6 exhibits solvent-dependent conformation in the crystalline state. Recrystallization from dichloromethane-n-pentane gave the anti conformation 6-anti, while recrystallization from methanol-acetone gave the syn conformation 6-syn, in which the three benzyl-o-carboranyl moieties are located to one side of the central benzene ring. Interestingly, one acetone molecule is captured in the π-rich space of 6-syn and two complexes facing each other encapsulate two acetone molecules in a π-rich container formed by the eight benzene rings. The inclusion involves several weak interactions, that is, T-shaped C-H···π interactions, and C-H···O and C-H···π interactions. Two C-H···O interactions involving benzylic C-H hydrogens activated by the electron-withdrawing character of the o-carborane cage and the oxygen atom of the acetone seem to be the most important. DFT calculations indicate that the binding energy for entrapment of acetone is 6.6 kcal/mol. Inclusion of acetone is achieved through not only multiple C-H···O interactions but also a number of C-H···π interactions. The third benzyl-o-carborane moiety is fixed in the syn conformation by intramolecular and intermolecular C-H···π interactions.

Calculation of absorption and emission spectra of [n]cycloparaphenylenes: the reason for the large Stokes shift.

The electronic absorption and emission spectra of the [n]cycloparaphenylenes with n = 6,7,...,11 ([n]CP) have been studied at the time-dependent density functional theory level. The calculations show that the optical gap increases with increasing size of the ring due to reduced ring strain in the larger carbon nanohoops, whereas the energy of the first bright state follows the opposite trend for the studied [n]CPs. For the excited-state structures, the C-C bonds between the phenylene groups have a significant double-bond character giving rise to a continuous electron delocalisation pathway around the ring. The torsion angles between the phenylene moieties are much smaller for the excited state than for the ground state suggesting that the excited state has a stronger electron delocalisation around the carbon nanohoop than for the ground state. The double bond character of the phenylene C-C bonds declines and the phenylene torsion angle increases with increasing ring size. The aromatic stabilisation of the excited state due to the continuous electron delocalisation pathway is probably the main reason for the large Stokes shift. The excited state of the larger [n]CPs are less aromatic than the smaller ones explaining why the Stokes shift decreases with increasing size of the ring. For large [n]CPs, the excitation-energy spectrum forms bands making localisation of the excitons feasible. Localisation of the excitons probably leads to the observed ring-size independence of the electronic excitation spectra for large [n]CPs.

Aromatic pathways in twisted hexaphyrins.

The aromatic pathways and the degree of aromaticity of expanded porphyrins have been determined by explicit calculations of the routes and strengths of the magnetically induced currents using the gauge-including magnetically induced current (GIMIC) approach. Density functional theory calculations show that the doubly twisted hexaphyrins fulfilling Hückel's (4n + 2) pi-electron rule for aromaticity and those obeying the 4n pi-electron rule for antiaromaticity are aromatic and antiaromatic, respectively. The investigated [26]hexaphyrin (2) and (3) and [30]hexaphyrin (5) isomers are aromatic, and [28]hexaphyrin (4) is antiaromatic. The formally antiaromatic [24]hexaphyrin (1) does not sustain any strong ring current and must be considered nonaromatic. A detailed analysis of the current pathways of the hexaphyrins is presented. It was found that the current pathways of the investigated aromatic hexaphyrins are not always dominated by the flow along the inner route through the non-hydrogenated C-N-C moieties, as previously proposed. The current flow is often split into two branches at the pyrrole rings, but sometimes it takes the outer route via the C=C bond of the pyrrole. The current pathway of the weak paratropic ring current of [24]hexaphyrin is dominated by the outer C=C route. The calculations show that the routes of the current transport cannot be assessed merely by inspection or from nucleus independent chemical shifts; explicit calculations of the current pathways are compulsory. The current-density studies also show that the pyrrole rings do not sustain any strong ring currents of their own.

Magnetically induced currents in bianthraquinodimethane-stabilized Möbius and Hückel [16]annulenes.

The ring currents, NMR chemical shifts, topology of the chemical bonding, and UV-vis spectra of bianthraquinodimethane-stabilized [16]annulenes possessing Möbius and Hückel topology are investigated. The aromatic character of the title compounds is discussed on the basis of the magnetically induced current density obtained using the gauge-including magnetically induced current (GIMIC) approach. Numerical integration of the current density circling around the [16]annulene ring shows that both the Hückel and the Möbius isomers are non-aromatic. The [16]annulene ring of both isomers sustains a net ring current whose strength is only 0.3 nA/T. The ring current consists of a diamagnetic flow on the outside of the [16]annulene ring and a paramagnetic current inside it. Since the net ring-current strength of the [16]annulene is less than 5% of the ring current strength for benzene, both isomers must be considered non-aromatic by the ring current criterion. The similar bond length alternation of the [16]annulene rings also points to a similarity in aromatic character of the two isomers. The shape of the ring current of the Möbius isomer shows that the current density is somewhat more outspread than that of the Hückel isomer. Spatially separated diatropic and paratropic currents of equal strength follow the annulene bonds. The atoms-in-molecules (AIM) analysis reveals a cage critical point in the region of the outspread current density of the Möbius isomer. Intramolecular CH...pi and pi-pi interactions identified by AIM analysis, in combination with the outspread current density, stabilizes the Möbius isomer relative to the Hückel one. The molecule is characterized by calculating the (13)C and (1)H NMR chemical shifts and the UV-vis spectrum and comparing these to experimental spectra. The (13)C NMR and (1)H NMR chemical shifts are rather similar for the two isomers. The UV-vis spectra are compared with the excitation energies calculated at the time-dependent density functional theory (TDDFT) level using Becke's three-parameter hybrid functional together with the LYP correlation functional (B3LYP), as well as at the approximate coupled cluster singles (CCS) and at the approximate coupled cluster singles and doubles (CC2) levels of theory. The CC2 calculations yield excitation energies in fairly good agreement with experimental data.

Probing the molecular and electronic structure of norhipposudoric and hipposudoric acids from the red sweat of Hippopotamus amphibius: a DFT investigation.

Molecular structure and tautomeric/conformational preferences of norhipposudoric and hipposudoric acids, the recently isolated pigments of the Hippopotamus amphibius' sweat, were investigated using the density functional theory (DFT) PBE0 formalism. Among a large variety of possible structures, two similar keto-enol tautomer/conformers are nearly isoenergetic and markedly more stable than the others both in the gas phase and aqueous solution. The bulk solvent effect was accounted for with the polarizable continuum model (PCM). A distinctive structural feature is the strong intramolecular hydrogen bonding in the keto-enol O-H...O bridge, as shown by analysis of the atoms-in-molecules topological properties of the electron density. To elucidate the claimed strong acidity of these pigments, the site-specific microscopic dissociation constants were also calculated using the cluster-continuum model, a hybrid approach based on inclusion of explicit solvent molecules and solvation of the cluster by the dielectric continuum. Notably, the first deprotonation should occur predominantly from the enolic group with a remarkably low pk(i) value. This factor could play an important role in the potent antibiotic activity of the pigments. The absorption spectra of the undissociated and dissociated compounds in aqueous solution were interpreted with time-dependent DFT/PCM calculations. The pi-pi* diquinoid excitations, mainly occurring in the fluorenoid nucleus, are the major contributors to the color and strong absorption bands in the UVA and UVB regions, which are closely related to the efficient sunscreen activity exerted by the pigments.

Molecular structure of the octatetranyl anion, C8H-: a computational study.

The equilibrium molecular structure of the octatetranyl anion, C8H(-), which has been recently detected in two astronomical environments, is investigated with the aid of both ab initio post-Hartree-Fock and density functional theory (DFT) calculations. The model chemistry adopted in this study was selected after a series of benchmark calculations performed on molecular acetylene for which accurate gas-phase structural data are available. Geometry optimizations performed at the CCSD/6-311+G(2d,p), QCISD/6-311+G(2d,p), and MP4(SDQ)/6-311+G(2d,p) levels of theory yield for C8H(-) an interesting polyyne-type structure that defies the chemical formula displaying a simple alternation of triple and single carbon-carbon bonds, [:C[triple bond]C-C[triple bond]C-C[triple bond]C-C[triple bond]CH](1-). In the optimized geometry of C8H(-), as one proceeds from the naked carbon atom on one side of the chain to the CH unit on the opposite side of the chain, the short (formally triple) carbon-carbon bonds decrease in length from 1.255 to 1.213 A whereas the long (formally single) carbon-carbon bonds increase (albeit only slightly) in length from 1.362 to 1.378 A (CCSD results). In striking contrast, both MP2 and DFT (B3LYP and PBE0) calculations fail in reproducing the pattern of the carbon-carbon bond lengths obtained with the CCSD, QCISD, and MP4 methods. The structures of three shorter n-even chains, C(n)H(-) (n = 2, 4, and 6), along with those of four n-odd compounds (n = 3, 5, 7, and 9) are also investigated at the CCSD/6-311+G(2d,p) level of theory.

Does Synergism in Microscopic Polarity Correlate with Extrema in Macroscopic Properties for Aqueous Mixtures of Dipolar Aprotic Solvents?

Aqueous mixtures of dipolar aprotic solvents (acetonitrile, γ-valerolactone, γ-butyrolactone, tetrahydrofuran, 1,4-dioxane, acetone, pyridine, N-methyl-2-pyrrolidone, N,N-dimethylformamide, N,N-dimethylacetamide, and dimethyl sulfoxide) show synergism in microscopic polarity and extrema in macroscopic viscosity (η) and molar excess enthalpy (HE) in water-rich compositions that correlate with solvent functional group electrostatic basicity (ß2H). Microscopic polarities of aqueous solvent mixtures were estimated by measuring the spectral shift (λmax) of 4-nitroaniline with UV-vis spectroscopy at 25 °C. Dynamic viscosities (η) and densities were measured for eight aqueous dipolar aprotic mixtures over the full range of compositions at (25 to 45) °C. The λmax, η, and HE values of the aqueous mixtures showed a linear trend with increasing electrostatic basicity of the solvent functional groups that is attributed to the size and strength of the hydration shell of water. Density functional theory (DFT) calculations were performed for 1:3 complexes (solvent: (H2O)3) and it was found that aqueous mixtures with high basicity have high binding energies and short hydrogen bonding distances implying that the size and strength of the hydration shell of water is proportional to functional group basicity. Consideration of functional group basicity of dipolar aprotic solvents allows one to relate synergism in microscopic polarity to extrema in macroscopic properties for a wide range of aqueous dipolar aprotic solvent mixtures.

Iodide and triiodide anion complexes involving anion-π interactions with a tetrazine-based receptor.

Protonated forms of the tetrazine ligand L2 (3,6-bis(morpholin-4-ylethyl)-1,2,4,5-tetrazine) interact with iodide in aqueous solution forming relatively stable complexes (ΔG° = -11.6(4) kJ mol-1 for HL2+ + I- = (HL2)I and ΔG° = -13.4(2) kJ mol-1 for H2L22+ + I- = [(H2L2)I]+). When solutions of [(H2L2)I]+ are left in contact with air, crystals of the oxidation product (H2L2)2(I3)3I·4H2O are formed. Unfortunately, the low solubility of I3- complexes prevents the determination of their stability constants. The crystal structures of H2L2I2·H2O (1), H2L2(I3)2·2H2O (2) and (H2L2)2(I3)3I·4H2O (3) were determined by means of X-ray diffraction analyses. In all crystal structures, it was found that the interaction between I- and I3- with H2L22+ is dominated by anion interactions with the π electron density of the receptor. Only in the case of 1, the iodide anions involved in close anion-π interactions with the ligand tetrazine ring form an additional H-bond with the protonated morpholine nitrogen of an adjacent ligand molecule. Conversely, in crystals of 2 and 3 there are alternate segregated planes which contain only protonated ligands hydrogen-bonded to cocrystallized water molecules or I3- and I- forming infinite two-dimensional networks established through short interhalogen contacts, making these crystalline products good candidates to behave as solid conductors. In the solid complexes, the triiodide anion displays both end-on and side-on interaction modes with the tetrazine ring, in agreement with density functional theory calculations indicating a preference for the alignment of the I3- molecular axis with the molecular axis of the ligand. Further information about geometries and structures of triiodide anions in 2 and 3 was acquired by the analysis of their Raman spectra.

Signal-transducing proteins for nanoelectronics.

This aim of this article is to provide novel paradigms for 21st century nanoelectronics by taking inspiration from the biology of signal transduction events where Nature has solved many complex problems, particularly those concerned with signal integration and amplification.

NMR and computational studies of the chemical reduction of [2.2]paracyclophane: formation of dianionic p-xylenyl oligomers.

Reaction of [2.2]paracyclophane with K/Na alloy in THF gives a p-xylylenyl dianion together with its dimer and trimer which are relatively stable at low temperatures; at ambient temperatures further polymerization takes place.

A quantum mechanical study on phosphotyrosyl peptide binding to the SH2 domain of p56lck tyrosine kinase with insights into the biochemistry of intracellular signal transduction events.

A study on the interaction between a phosphotyrosyl peptide with the SH2 domain of Lck kinase has been undertaken with the aid of semiempirical linear-scaling quantum mechanical methods. The structure of this complex has been solved at atomic resolution and, hence, it represents the ideal candidate for studying the charge deformation effects induced by the phosphopeptide on the binding site. Substantial changes in the charge of amino acid residues located in the binding pocket of the protein are observed upon ligand binding. More specifically, our quantum chemical calculations indicate that H-bonds involving charged side-chains are subject to consistent charge deformation effects whereas those forming salt bridges are unaffected by ligand binding. Furthermore, ligand binding has the effect of changing both the magnitude and direction of the protein's macrodipole, which rotates approximately 150 degrees with respect that of the unliganded protein. This suggests that a change in the polarization state of the protein might acts as a switch during the transmission of intracellular signals. The binding energy calculated with the aid of the COSMO solvation model corresponds to about -200 kcal/mol, most of which is attributed to the interaction of the phosphotyrosine head with the amino acid chains located in the binding site of the SH2 domain.

DFT study of caesium ion complexation by cucurbit[n]urils (n = 5-7).

Using density functional theory (DFT) calculations and the available crystallographic data we have investigated the binding of hydrated Cs(+) ions to the pumpkin-shaped cucurbituril macrocycles, CB[n] with n = 5-7. The calculations indicate that besides the interactions between caesium ions and the carbonyl-laced portals, also the hydrogen bonds established between the coordinated water molecules and the macrocycle do contribute to the overall binding affinity. Although the other alkali metal ions compete for binding with caesium, the partial dehydration of the caesium aqua ions is likely favoured by the relatively small interaction energy associated with the water-Cs(+) bond. The inclusion inside the macrocycle's cavity of either one water molecule or one chloride anion enhances the binding of Cs(+) due to the additional ion-dipole or ion-ion interactions, respectively, established within the complexes. An advantage in using cucurbituril macrocycles for the sequestration of caesium ions from an aqueous solution is the possibility of binding two hydrated metal ions by the carbonyl-laced portals thereby forming 1 : 2 complexes.