Analysis of the origin of through-space proton NMR deshielding by selected organic functional groups

Pillar[5]arene-Derived endo-Functionalized Molecular Tube for Mimicking Protein-Ligand Interactions

Artificial tubular molecular pockets bearing polar functionalities on their inner surface are useful model systems for understanding the mechanisms of protein-ligand interactions in living systems. We herein report a pillar[5]arene-derived molecular tube, [P4-(OH)BPO], whose endo conformational isomer endo-[P4-(OH)BPO] possesses an inwardly pointing hydrogen-bond (H-bond) donor (OH) in its deep cavity and a strong H-bond acceptor (C═O) on its predominantly hydrophobic inner surface, rendering it a perfect protein binding pocket mimetic. A fragment-based drug design model was established using endo-[P4-(OH)BPO] and a library of various shape-complementary fragment ligands (1-38). On the basis of the binding affinity data for "fragment-pocket" complexes G⊂endo-[P4-(OH)BPO] (G = 1-38), two rationally designed "lead molecules" (39 and 40) were identified as being able to enhance binding affinity significantly by forming H-bonds with both the donor and acceptor of endo-[P4-(OH)BPO]. The described work opens new avenues for developing pillar[n]arene-derived protein binding pocket-mimetic systems for studies of protein-ligand interactions and mechanisms of enzymatic reactions.

[4]Cyclofluorene: Unexpected Influence of Alkyl Chain Length

Presented here is the study of a new example of [4]cyclofluorene, with ethyl chains on the bridgeheads. Its molecular structure was established by solution NMR spectroscopy and single-crystal X-ray diffraction. Three successive oxidation processes and one reversible reduction were observed through cyclic voltammetry. The optical properties were characterized both in solution and thin film by UV/visible spectroscopy as well as stationary and time-resolved fluorescence. It was found that this [4]cyclofluorene displays different characteristics compared with the other [4]cyclofluorenes substituted by methyl or propyl chains: a simple modification of the chain length induces a non-negligible effect on the emission properties, which must be linked to the specific arrangement of the fluorene units. Furthermore, single-crystal X-ray diffraction reveals the formation of a pseudo-tubular solid-state arrangement of fully symmetrical ring structures, which was not observed for the other members of the [4]cyclofluorenes family. This finding could open the way to modulation of properties of cyclofluorenes through alkyl chain engineering.

Benzonitrile Oxide Cycloadditions with Exocyclic Methylene Benzothiazepine Dioxides

N-substituted 5-methylene-2,3,4,5-tetrahydrobenzo[f][1,2]thiazepine 1,1-dioxides underwent 1,3-dipolar cycloaddition with benzonitrile oxide, generated in situ, to give isoxazoline spiro adducts. The cycloadditions were completely regioselective to give the hitherto unreported 3,4-dihydro-2H,4′H-spiro[benzo[f][1,2]thiazepine-5,5′-isoxazole] 1,1-dioxide cycloadduct. Where the N-substituent on the sulfonamide cycloaddition precursor was a 2-substituted arene, the resulting atropisomerism along the N-aryl bond led to facial selectivity in the cycloaddition reaction, with greater than 90 % diastereoselectivity.

Chemical bonding and aromaticity in furan, pyrrole, and thiophene: a magnetic shielding study

Aromaticity and bonding in furan, pyrrole, and thiophene are investigated through the behavior of the isotropic shielding σiso(r) within the regions of space surrounding these molecules. HF-GIAO/6-311++G(d,p) and MP2-GIAO/6-311++G(d,p) (Hartree-Fock and second-order Møller-Plesset perturbation theory utilizing gauge-including atomic orbitals) σiso(r) contour plots are constructed using regular two-dimensional 0.05 Å grids in the molecular plane, in horizontal planes 0.5 and 1 Å above it, and in a vertical plane through the heteroatom. The nucleus-independent chemical shifts (NICS) calculated at the ring centers and at 0.5 Å and 1 Å above these centers, NICS(0), NICS(0.5), and NICS(1), respectively, support the widely accepted order of aromaticities thiophene > pyrrole > furan. The results suggest that accurate NICS calculations benefit more from the use of an extended basis set than from the inclusion of dynamical electron correlation effects. The different extents of σiso(r) delocalization observed in the horizontal contour plots and other features of σiso(r) are also consistent with an aromaticity reduction of the order thiophene > pyrrole > furan. It is suggested that the extent of σiso(r) delocalization in σiso(r) contour plots in planes 1 Å above the molecular plane could be used for comparing the relative aromaticities of a wide range of aromatic systems.

Is the conventional interpretation of the anisotropic effects of C=C double bonds and aromatic rings in NMR spectra in terms of the π-electron shielding/deshielding contributions correct?

Based on the nucleus-independent chemical shift (NICS) concept, isotropic magnetic shielding values have been computed along the three Cartesian axes for ethene, cyclobutadiene, benzene, naphthalene, and benzocyclobutadiene, starting from the molecular/ring center up to 10 Å away. These through-space NMR spectroscopic shielding (TSNMRS) values, which reflect the anisotropic effects, have been broken down into contributions from localized- and canonical molecular orbitals (LMOs and CMOs); these contributions revealed that the proton NMR spectroscopic chemical shifts of nuclei that are spatially close to the C=C double bond or the aromatic ring should not be explained in terms of the conventionally accepted π-electron shielding/deshielding effects. In fact, these effects followed the predictions only for the antiaromatic cyclobutadiene ring.

Computation of through-space NMR shielding effects by small-ring aromatic and antiaromatic hydrocarbons

The GIAO-HF method in Gaussian 03 was employed to calculate the isotropic NMR shielding values of a diatomic hydrogen probe above simple small-ring aromatic and antiaromatic hydrocarbons, including neutral and ionic examples. Subtraction of the isotropic shielding of diatomic hydrogen by itself allowed the prediction of through-space proton NMR shielding increment surfaces for these systems. Substantial shielding was observed above the center of aromatic rings, regardless of whether the ring was pi-aromatic or sigma-aromatic, and also regardless of the charge. In sharp contrast, deshielding was observed above the center of antiaromatic rings, regardless of whether the ring was pi-aromatic or sigma-aromatic, and also regardless of the charge. Shielding increment values at 2.5 angstrom above the ring centers were compared to NICS values at the same position. The shielding effects predicted by using diatomic hydrogen as a computational probe are diagnostic of whether a structure possesses aromaticity or antiaromaticity.

Quantification of the Push−Pull Effect in Tolanes and a Revaluation of the Factors Affecting the 13C Chemical Shifts of the Carbon Atoms of the C⋮C Triple Bond

Variously substituted tolanes were employed to show that the push-pull effect is also active in CC triple bonds by the successful correlation of the occupation quotient pi/pi of the pi orbital in resonance with the substituted phenyl moieties of tolanes versus the bond length of the CC triple bond. In addition, the influences of the ortho phenyl ring substituents on the 13C chemical shifts of the triple bond carbon atoms, which were estimated by Rubin et al.(4) to be "inapplicable for describing triple bond polarization", were re-evaluated, leading to the conclusion that, while anisotropic effects of ortho substituents are negligible, the steric ortho-substituent effects do in fact dominate the deviations obtained. A detailed theoretical NBO/NCS study has been employed to illuminate the facts of this case.

Current Densities and Nucleus-Independent Chemical Shift Maps from Reciprocal-Space Density Functional Perturbation Theory Calculations

A method to calculate condensed-matter nucleus independent chemical shift maps (NICS maps) from first principles in the framework of density functional theory is presented. I use a pseudopotential plane-wave approach in which the electronic current density and the NICS map are obtained from an inverse Fourier transformation of the induced magnetic field represented in reciprocal space (G space). Due to its intrinsically periodic description, the method is suitable for isolated molecules (by using a supercell technique) and for condensed-phase systems like solids. The periodic NICS method was applied to hydrogen-bonded calixhydroquinone nanotubes, crystalline graphite, and two carbon nanotube systems.

A comparison of calculated NMR shielding probes

In a strong magnetic field, covalently bonded hydrogen nuclei located over the plane of an anisotropic pi bond-containing functional group experience magnetic shielding (or deshielding) that results from the combined effect of the magnetic anisotropy of the functional group and other nearby covalent bonds plus other intramolecular shielding effects. These effects can now be calculated with reasonable accuracy using ab initio methods. We have investigated several computational probes of the magnetic shielding surface near anisotropic functional groups and compared the results to previous reports of experimental observations in example structures. GIAO-HF in Gaussian 03 was employed to calculate isotropic shielding values and to predict the net NMR shielding increment for several computational probes: methane, diatomic hydrogen, a hydrogen atom, a helium atom, or a ghost atom, each held in various positions over simple test molecules (ethene, ethyne, benzene and HCN) that contain the functional groups studied. Also, the effect of performing single point calculations versus constrained geometry-optimized calculations was examined. In addition, the effect of the angle of the orientation of the probe molecule (in the case of CH(4) and H(2)) relative to the pi bond in the test molecule was studied. Finally, the atomic charges in the molecular probes (CH(4) and H(2)) were computed to investigate the nature of the interaction of the probe with the test molecule. The optimal, most economical computational results were obtained using single point calculations of a diatomic hydrogen probe oriented perpendicular to the surface (or axis) of the test molecule.

Separation of Anisotropic and Steric Substituent Effects−Nuclear Chemical Shielding Analysis of H-4 and C-4 in Phenanthrene and 11-Ethynylphenanthrene

The anisotropic effect of a proximally introduced ethynyl group on the chemical shifts of H-4 and C-4 of the phenanthrene skeleton was calculated using GIAO-HF/NICS methodology. The anisotropic effect, long considered to be the source of the considerable downfield shift of H-4 in 11-ethynylphenanthrene in comparison to the chemical shift value of the corresponding proton in phenanthrene, was determined to be only negligible in magnitude on the basis of these calculations. Partitioning of the natural chemical shieldings of H-4 and C-4 by the NCS-NBO method into various contributions from the C-C and C-H bonds present in each molecule revealed that steric compression was able to account for the large downfield shifts of both H-4 and C-4 in 11-ethynylphenanthrene relative to phenanthrene. Thus, the substituent effect is almost totally permeated by this latter interaction and not by the aforementioned process, which was previously presumed to be the sole underlying cause.

An NMR shielding model for protons above the plane of a carbonyl group

Covalently bonded hydrogen nuclei located over the plane of a carbonyl group in a strong magnetic field experience magnetic shielding (or deshielding) that results from the combined effect of the magnetic anisotropy of the carbon-oxygen double bond and various other intramolecular shielding effects. GIAO-HF in Gaussian 98 was employed to calculate isotropic shielding values and to predict the net proton NMR shielding increment for a simple model system: the proximate proton of methane held in various positions over formaldehyde. The net shielding increments of the proximate proton of methane, plotted against its Cartesian coordinates relative to the center of the carbon-oxygen double bond, led to the development of a single empirical equation for predicting the NMR shielding experienced by a covalently bonded proton over the plane of a carbonyl group. The predictive capability of this equation has been validated by calculating the shielding increments of protons over the plane of a carbonyl group in known structures, using this as a correction to the chemical shift estimated by subtituent effects and comparing the result to experimentally observed chemical shifts. Shielding is predicted by this equation for protons located in the region from over the center of the carbon-oxygen double bond to beyond the carbon atom; deshielding is predicted for protons located above and beyond the oxygen atom. This prediction differs from those made by the long-held "shielding cone" model found in nearly every textbook on NMR, but is consistent with experimental observations. The algorithm for predicting the shielding increment for a proton over a carbonyl group can be used in a spreadsheet or incorporated into software that estimates chemical shifts using additive substituent constants or a database of structures. Its use can improve the accuracy of the estimated chemical shift of a proton in the vicinity of a carbon-oxygen double bond, and thus assist in spectral assignments and in correct structure determination.

Complexation-induced chemical shifts--ab initio parameterization of transferable bond anisotropies

Complexation-induced changes in proton chemical shifts provide a potent tool for conformational analysis, being highly dependent on intermolecular orientation. An important contribution to these shifts arises from the molecular magnetisability anisotropy, or more specifically from the anisotropy of certain groups, such as aromatic rings and unsaturated bonds. While the influence of aromatic rings has been well characterised via the ring current effect, unsaturated bonds have received much less attention and prediction of complexation shifts is hampered by the lack of accurate anisotropy parameters for these bonds. We have therefore used ab initio calculations at the HF/aug-cc-pVDZ level to obtain bond anisotropies for C-H, N-H, C=O, C=C, C triple bond N, N=N, C triple bond C, and C triple bond N. Fitting the anisotropies to bond magnetic dipoles (the McConnell equation) gives non-transferable values for C-H and N-H bonds. We have therefore expanded in terms of bond magnetic dipoles, quadrupoles, and octopoles for double and triple bonds only, obtaining highly accurate shielding surfaces in all cases. The transferable nature of the anisotropies is confirmed by comparing with shifts obtained in larger molecules containing unsaturated bonds.

How do ring currents affect (1)h NMR chemical shifts?

Conventional explanations of proton NMR chemical shifts need fundamental revisions. Ab initio (IGLO) analyses reveal that the downfield delta (1)H of benzene is not due to deshielding ring current effects; the shielding is less than the pi contribution to vinyl delta (1)Hs. Enhanced deshielding sigma CC influences are responsible for the more downfield delta (1)Hs of the inner protons of naphthalene and anthracene. Double pi effects shield ethynyl Hs; there is no evidence for a special "ring current influence."

Aromaticity with a twist: Möbius [4n]annulenes

Aromatic Möbius [4n]annulenes with 4n pi electrons, originally conceived by Heilbronner, are characterized computationally. These (CH)(12), (CH)(16), and (CH)(20) minima have nearly equal C-C bond lengths, small twist angles around the rings, and magnetic properties (NICS, nucleus-independent chemical shifts--see above at various positions in [16]annulene--and magnetic susceptibility exaltations) indicating significantly diatropic ring currents. The Möbius forms are not the most stable isomers but may contribute significantly to the chemistry of these annulenes. [structure: see text]

Modeling through-space magnetic shielding over ethynyl, cyano, and nitro groups

In a strong magnetic field, covalently bonded hydrogen nuclei located over a pi bonded functional group experience magnetic shielding (or deshielding) that results from the combined effect of the magnetic anisotropy of the pi bond and various other intramolecular shielding effects. Gauge including atomic orbital (GIAO)-HF in Gaussian 98 was employed to calculate isotropic shielding values and to predict the net through-space proton NMR shielding increment for a simple model system: the proximate proton of methane held in various positions over simple molecules that contain a carbon-carbon triple bond, a carbon-nitrogen triple bond, or a nitro group. These net shielding increments of the proximate proton of methane, plotted against their Cartesian coordinates, led to the development of a single empirical equation for predicting the NMR shielding experienced by a covalently bonded proton over each group. The predictive capability of each equation has been validated by calculating shielding increments of protons over the functional group in known structures. These shielding increments are then used to adjust predicted chemical shifts for through-space shielding effects, and the adjusted values are compared to experimentally observed chemical shifts. The algorithms for predicting the shielding increment for a proton over these functional groups can be used in a spreadsheet or incorporated into software that estimates chemical shifts using additive substituent constants or a database of structures. Their use can substantially improve the accuracy of the estimated chemical shift of a proton in the vicinity of these functional groups, and thus assist in spectral assignments and in correct structure determination.