David L. Bryce

Direct detection of CH/π interactions in proteins

XH/pi interactions make important contributions to biomolecular structure and function. These weakly polar interactions, involving pi-system acceptor groups, are usually identified from the three-dimensional structures of proteins. Here, nuclear magnetic resonance spectroscopy has been used to directly detect methyl/pi (Me/pi) interactions in proteins at atomic resolution. Density functional theory calculations predict the existence of weak scalar (J) couplings between nuclei involved in Me/pi interactions. Using an optimized isotope-labelling strategy, these J couplings have been detected in proteins using nuclear magnetic resonance spectroscopy. The resulting spectra provide direct experimental evidence of Me/pi interactions in proteins and allow a simple and unambiguous assignment of donor and acceptor groups. The use of nuclear magnetic resonance spectroscopy is an elegant way to identify and experimentally characterize Me/pi interactions in proteins without the need for arbitrary geometric descriptions or pre-existing three-dimensional structures.

A revised experimental absolute magnetic shielding scale for oxygen

A revised absolute magnetic shielding scale for oxygen is established based on a recently reported highly precise experimental measurement of the 17O spin-rotation constant in carbon monoxide. The isotropic oxygen magnetic shielding constant for 12C17O at the equilibrium geometry, σe, is found to be −56.8±0.6 ppm. The experimental rovibrationally averaged value of the shielding constant at 300 K, 〈σ〉300 K, is −62.7±0.6 ppm, in excellent agreement with the ab initio value reported by Vaara et al. [J. Chem. Phys. 109, 8388 (1998)]. Based on the revised scale and on experimentally known oxygen chemical shifts, 〈σ〉300 K (H2O(l)) is 287.5±0.6 ppm and 〈σ〉300 K (H2O(g)) is 323.6±0.6 ppm.

Calcium-43 Chemical Shift Tensors as Probes of Calcium Binding Environments. Insight into the Structure of the Vaterite CaCO3 Polymorph by 43Ca Solid-State NMR Spectroscopy

Natural-abundance (43)Ca solid-state NMR spectroscopy at 21.1 T and gauge-including projector-augmented-wave (GIPAW) DFT calculations are developed as tools to provide insight into calcium binding environments, with special emphasis on the calcium chemical shift (CS) tensor. The first complete analysis of a (43)Ca solid-state NMR spectrum, including the relative orientation of the CS and electric field gradient (EFG) tensors, is reported for calcite. GIPAW calculations of the (43)Ca CS and EFG tensors for a series of small molecules are shown to reproduce experimental trends; for example, the trend in available solid-state chemical shifts is reproduced with a correlation coefficient of 0.983. The results strongly suggest the utility of the calcium CS tensor as a novel probe of calcium binding environments in a range of calcium-containing materials. For example, for three polymorphs of CaCO3 the CS tensor span ranges from 8 to 70 ppm and the symmetry around calcium is manifested differently in the CS tensor as compared with the EFG tensor. The advantages of characterizing the CS tensor are particularly evident in very high magnetic fields where the effect of calcium CS anisotropy is augmented in hertz while the effect of second-order quadrupolar broadening is often obscured for (43)Ca because of its small quadrupole moment. Finally, as an application of the combined experimental-theoretical approach, the solid-state structure of the vaterite polymorph of calcium carbonate is probed and we conclude that the hexagonal P6(3)/mmc space group provides a better representation of the structure than does the orthorhombic Pbnm space group, thereby demonstrating the utility of (43)Ca solid-state NMR as a complementary tool to X-ray crystallographic methods.

Capsule formation, carboxylate exchange, and DFT exploration of cadmium cluster metallocavitands: highly dynamic supramolecules.

A family of molecular heptacadmium carboxylate clusters templated inside [3 + 3] Schiff base macrocycles has been isolated and studied by variable temperature solution and solid-state NMR spectroscopy, single-crystal X-ray diffraction (SCXRD), and density functional theory (DFT) calculations. These metallocavitand cluster complexes adopt bowl-shaped structures, induced by metal coordination, giving rise to interesting host-guest and supramolecular phenomena. Specifically, dimerization of these metallocavitands yields capsules with vacant coordination and hydrogen-bonding sites accessible to encapsulated guests. Strong host-guest interactions explain the exceptionally high packing coefficient (0.80) observed for encapsulated N,N-dimethylformamide (DMF). The guest-accessible hydrogen-bonding sites arise from an unusual mu(3)-OH ligand bridging three cadmium ions. Thermodynamic and kinetic studies show that dimerization is an entropy-driven process with a highly associative mechanism. In DMF the exchange rate of peripheral cluster supporting carboxylate ligands is intrinsically linked to the rate of dimerization and these two seemingly different events have a common rate-determining step. Investigation of guest dynamics with solid-state (2)H NMR spectroscopy revealed 3-fold rotation of an encapsulated DMF molecule. These studies provide a solid understanding of the host-guest and dynamic properties of a new family of metallocavitands and may help in designing new supramolecular catalysts and materials.

Direct investigation of covalently bound chlorine in organic compounds by solid-state 35Cl NMR spectroscopy and exact spectral line-shape simulations.

35/37Cl NMR spectroscopy studies of organic systems are very rare, with only a few neat liquids having been studied.1 The lack of chlorine NMR spectroscopy data may be explained by the fact that 35Cl and 37Cl are quadrupolar (spin I=3/2) and low-frequency isotopes. The quadrupole moments of the chlorine nuclei couple with the electric field gradient (EFG) tensor at the nuclei; this phenomenon is known as the quadrupolar interaction (QI). The quadrupolar coupling constant, CQ, and the quadrupolar asymmetry parameter, ηQ, describe the magnitude and asymmetry of the QI. In solution, one of the consequences of the QI is fast relaxation, which means that the 35/37Cl NMR signals for covalently bound chlorines are very broad and are of low intensity.1 For these reasons, chemically distinct chlorine sites are very difficult to distinguish with solution NMR spectroscopy. However, in the solid state, nuclear spin relaxation is typically slower, thus enabling higher quality 35Cl NMR spectra to be collected, at least in principle. Unfortunately, the magnitude of the QI for covalently bound chlorines is very large because of the substantial, anisotropic EFG at the Cl atom, owing mainly to its electronic configuration when it forms a chlorine–carbon bond. Conventional wisdom is that such chlorine sites cannot be studied in powders by solid-state NMR spectroscopy as the central transition (CT; mI=1/2↔−1/2) can span tens of megahertz in typical commercially available magnetic fields. For this reason, only ionic chlorides2 and inorganic chlorides3 have been studied, as the EFG at these chlorides is often an order of magnitude smaller than at covalently bound chlorine atoms in organic molecules. The bonding environments for these types of chlorine atoms are substantially different from the environments in those chloride-containing molecules that have been studied previously.2, 3 A partial 35Cl NMR spectrum for hexachlorophene has been briefly mentioned in the literature.4 On the other hand, most of the interesting chlorine chemistry occurs when Cl is covalently bound to a carbon atom, where the chlorine atom often acts as a leaving group. Chlorine atoms are also important in many organic pharmaceuticals as well as in crystal design applications where they can form halogen bonds.5 Recent studies show that covalently bound chlorine is also important in biological chemistry where, for example, the tryptophan 7-halogenase was found to selectively chlorinate tryptophan moieties.6

QUEST—QUadrupolar Exact SofTware: A fast graphical program for the exact simulation of NMR and NQR spectra for quadrupolar nuclei

We present a new program for the exact simulation of solid-state NMR spectra of quadrupolar nuclei in stationary powdered samples which employs diagonalization of the combined Zeeman-quadrupolar Hamiltonian. The program, which we call QUEST (QUadrupolar Exact SofTware), can simulate NMR spectra over the full regime of Larmor and quadrupolar frequency ratios, which encompasses scenarios ranging from high-field NMR to nuclear quadrupole resonance (NQR, where the Larmor frequency is zero) and does not make use of approximations when treating the quadrupolar interaction. With the use of the fast powder averaging scheme of Alderman, Solum, and Grant, exact NMR spectral simulations are only marginally slower than the second-order perturbation theory counterpart. The program, which uses a graphical user interface, also incorporates chemical shift anisotropy and non-coincident chemical shift and quadrupolar tensor frames. The program is validated against newly-acquired experimental data through several examples including: the low-field (79/81)Br NMR spectra of CaBr(2), the (14)N overtone NMR spectrum of glycine, the (187)Re NQR spectra of Re(2)(CO)(10), and lastly the (127)I overtone NQR spectrum of SrI(2), which, to the best of our knowledge, represents the first direct acquisition of an overtone NQR spectrum for a powdered sample.

A Solid-State 11B NMR and Computational Study of Boron Electric Field Gradient and Chemical Shift Tensors in Boronic Acids and Boronic Esters

The results of a solid-state 11B NMR study of a series of 10 boronic acids and boronic esters with aromatic substituents are reported. Boron-11 electric field gradient (EFG) and chemical shift (CS) tensors obtained from analyses of spectra acquired in magnetic fields of 9.4 and 21.1 T are demonstrated to be useful for gaining insight into the molecular and electronic structure about the boron nucleus. Data collected at 21.1 T clearly show the effects of chemical shift anisotropy (CSA), with tensor spans (Ω) on the order of 10−40 ppm. Signal enhancements of up to 2.95 were achieved with a DFS-modified QCPMG pulse sequence. To understand the relationship between the measured tensors and the local structure better, calculations of the 11B EFG and magnetic shielding tensors for these compounds were conducted. The best agreement was found between experimental results and those obtained from GGA revPBE DFT calculations. A positive correlation was found between Ω and the dihedral angle (ϕCCBO), which describes the orientation of the boronic acid/ester functional group relative to an aromatic system bound to boron. The small boron CSA is discussed in terms of paramagnetic shielding contributions as well as diamagnetic shielding contributions. Although there is a region of overlap, both Ω and the 11B quadrupolar coupling constants tend to be larger for boronic acids than for the esters. We conclude that the span is generally the most characteristic boron NMR parameter of the molecular and electronic environment for boronic acids and esters, and show that the values result from a delicate interplay of several competing factors, including hydrogen bonding, the value of ϕCCBO, and the electron-donating or withdrawing substituents bound to the aromatic ring.

Signal enhancement in solid-state NMR of quadrupolar nuclei

Recent progress in the development and application of signal enhancement methods for NMR of quadrupolar nuclei in solids is presented. First, various pulse schemes for manipulating the populations of the satellite transitions in order to increase the signal of the central transition (CT) in stationary and rotating solids are evaluated (e.g., double-frequency sweeps, hyperbolic secant pulses). Second, the utility of the quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) and WURST-QCPMG pulse sequences for the rapid and efficient acquisition of particularly broad CT powder patterns is discussed. Third, less frequently used experiments involving polarization transfer from abundant nuclear spins (cross-polarization) or from unpaired electrons (dynamic nuclear polarization) are assessed in the context of recent examples. Advantages and disadvantages of particular enhancement schemes are highlighted and an outlook on possible future directions for the signal enhancement of quadrupolar nuclei in solids is offered.

Potent inhibition of ice recrystallization by low molecular weight carbohydrate-based surfactants and hydrogelators

Ice recrystallization inhibition (IRI) activity is a very desirable property for an effective cryoprotectant. This property was first observed in biological antifreezes (BAs), which cannot be utilized in cryopreservation due to their ability to bind to ice. To date, potent IRI active compounds have been limited to BAs or synthetic C-linked AFGP analogues (1 and 2), all of which are large peptide-based molecules. This paper describes the first example of low molecular weight carbohydrate-based derivatives that exhibit potent IRI activity. Non-ionic surfactant n-octyl-β-D-galactopyranoside (4) exhibited potent IRI activity at a concentration of 22 mM, whereas hydrogelator N-octyl-D-gluconamide (5) exhibited potent IRI activity at a low concentration of 0.5 mM. Thermal hysteresis measurements and solid-state NMR experiments indicated that these derivatives are not exhibiting IRI activity by binding to ice. For non-ionic surfactant derivatives (3 and 4), we demonstrated that carbohydrate hydration is important for IRI activity and that the formation of micelles in solution is not a prerequisite for IRI activity. Furthermore, using solid-state NMR and rheology we demonstrated that the ability of hydrogelators 5 and 6 to form a hydrogel is not relevant to IRI activity. Structure–function studies indicated that the amide bond in 5 is an essential structural feature required for potent IRI activity.

Liquid-crystal NMR structure of HIV TAR RNA bound to its SELEX RNA aptamer reveals the origins of the high stability of the complex

Transactivation-response element (TAR) is a stable stem–loop structure of HIV RNA, which plays a crucial role during the life cycle of the virus. The apical loop of TAR acts as a binding site for essential cellular cofactors required for the replication of HIV. High-affinity aptamers directed against the apical loop of TAR have been identified by the SELEX approach. The RNA aptamers with the highest affinity for TAR fold as hairpins and form kissing complexes with the targeted RNA through loop–loop interactions. The aptamers with the strongest binding properties all possess a GA base pair combination at the loop-closing position. Using liquid-crystal NMR methodology, we have obtained a structural model in solution of a TAR–aptamer kissing complex with an unprecedented accuracy. This high-resolution structure reveals that the GA base pair is unilaterally shifted toward the 5′ strand and is stabilized by a network of intersugar hydrogen bonds. This specific conformation of the GA base pair allows for the formation of two supplementary stable base-pair interactions. By systematic permutations of the loop-closing base pair, we establish that the identified atomic interactions, which form the basis for the high stability of the complex, are maintained in several other kissing complexes. This study rationalizes the stabilizing role of the loop-closing GA base pairs in kissing complexes and may help the development or improvement of drugs against RNA loops of viruses or pathogens as well as the conception of biochemical tools targeting RNA hairpins involved in important biological functions.