Experimental and Theoretical Determination of Nucleic Acid Magnetic Susceptibility: Importance for the Study of Dynamics by Field-Induced Residual Dipolar Couplings

Magnetic susceptibility anisotropies (Deltachi) are determined for the nucleic acid bases on the basis of a combined NMR spectroscopic and DFT study. Magnetic field-induced residual dipolar couplings (RDC) measured for the Dickerson dodecamer allow for the determination of a precise value of Deltachi for this DNA. A tensor summation employing the results of DFT calculations of the individual base magnetic susceptibility tensors and the known structure of the dodecamer provides a value of Deltachi which is in excellent agreement with experiment. The DFT results are shown to provide superior agreement with experiment for the dodecamer and a protein-DNA complex when compared with other sets of values in common use in the literature. The marked discrepancy between our Deltachi values and existing sets of values has a direct and significant impact on the interpretation of field-induced anisotropic interactions in terms of biomolecular structure and dynamics.

Measurement of five dipolar couplings from a single 3D NMR multiplet applied to the study of RNA dynamics

A new three-dimensional NMR experiment is described that yields five scalar or dipolar couplings from a single cross-peak between three spins. The method is based on the E.COSY principle and is demonstrated for the H1'-C1'-C2' fragment of ribose sugars in a uniformly 13C-enriched 24-nucleotide RNA stem-loop structure, for which a complete set of couplings was obtained for all nonmodified nucleotides. The values of the isotropic J couplings and the 13C1' and 13C2' chemical shifts define the sugar pucker. Once the sugar pucker is known, the five dipolar couplings between C1'-H1', C2'-H2', H1'-H2', C1'-H2', and C2'-H1', together with C1'-C2', C3'-H3', and C4'-H4' available from standard experiments, can be used to derive the five unknowns that define the local alignment tensor, thereby simultaneously providing information on relative orientation and dynamics of the ribose units. Data indicate rather uniform alignment for all stem nucleotides in the 24-nt stem-loop structure, with only a modest reduction in order for the terminal basepair, but significantly increased mobility in part of the loop region. The method is applicable to proteins, nucleic acids, and carbohydrates, provided 13C enrichment is available.

Application of correlated residual dipolar couplings to the determination of the molecular alignment tensor magnitude of oriented proteins and nucleic acids

Residual dipolar couplings (RDC) between nuclear spins in partially aligned samples offer unique insights into biomacromolecular structure and dynamics. To fully benefit from the RDC data, accurate knowledge of the magnitude ( D (a)) and rhombicity ( R ) of the molecular alignment tensor, A, is important. An extended histogram method (EHM) is presented which extracts these parameters more effectively from dipolar coupling data. The method exploits the correlated nature of RDCs for structural elements of planar geometry, such as the one-bond (13)C'(i)-(13)C(i)(alpha), (13)C'(i)-(15)N(i+1), and (15)N(i+1)-(1)H(N)(i+1) couplings in peptide bonds of proteins, or suitably chosen combinations of (1) D (C1'H1'), (1) D (C2'H2'), (1) D (C1'C2'), (2) D (C2'H1'), (2) D (C1'H2'), and (3) D (H1'H2') couplings in nucleic acids, to generate an arbitrarily large number of synthetic RDCs. These synthetic couplings result in substantially improved histograms and resulting values of D (a) and R, compared with histograms generated solely from the original sets of correlated RDCs, particularly when the number of planar fragments for which couplings are available is small. An alternative method, complementary to the EHM, is also described, which uses a systematic grid search procedure, based on least-squares fitting of sets of correlated RDCs to structural elements of known geometry, and provides an unambiguous lower limit for the degree of molecular alignment.

An 17O NMR and quantum chemical study of monoclinic and orthorhombic polymorphs of triphenylphosphine oxide

Solid-state (17)O NMR spectroscopy is employed to characterize powdered samples of known monoclinic and orthorhombic modifications of (17)O-enriched triphenylphosphine oxide, Ph(3)PO. Precise data on the orientation-dependent (17)O electric field gradient (EFG) and chemical shift (CS) tensors are obtained for both polymorphs. While the (17)O nuclear quadrupolar coupling constants (C(Q)) are essentially identical for the two polymorphs (C(Q) = -4.59 +/- 0.01 MHz (orthorhombic); C(Q) = -4.57 +/- 0.01 MHz (monoclinic)), the spans (Omega) of the CS tensors are distinctly different (Omega = 135 +/- 3 ppm (orthorhombic); Omega = 155 +/- 5 ppm (monoclinic)). The oxygen CS tensor is discussed in terms of Ramsey's theory and the electronic structure of the phosphorus-oxygen bond. The NMR results favor the hemipolar sigma-bonded R(3)P(+)-O(-) end of the resonance structure continuum over the multiple bond representation. Indirect nuclear spin-spin (J) coupling between (31)P and (17)O is observed directly in (17)O magic-angle-spinning (MAS) NMR spectra as well as in (31)P MAS NMR spectra. Ab initio and density-functional theory calculations of the (17)O EFG, CS, and (1)J((31)P,(17)O) tensors have been performed with a variety of basis sets to complement the experimental data. This work describes an interesting spin system for which the CS, quadrupolar, J, and direct dipolar interactions all contribute significantly to the observed (17)O NMR spectra and demonstrates the wealth of information which is available from NMR studies of solid materials.

Microwave spectroscopy and nuclear magnetic resonance spectroscopy--what is the connection?

The history and development of microwave spectroscopy and nuclear magnetic resonance (NMR) spectroscopy have much in common. In this Account, we discuss the less widely appreciated connections between the parameters measured using the two techniques. Selected examples from our laboratory and from the recent literature attest to the utility and importance of these connections. For example, how are nuclear spin-rotation tensors and NMR chemical shifts related? Why should chemists be interested in absolute magnetic shielding scales? What can chemists learn about trends in spin-spin coupling constants from the hyperfine parameters measured in microwave and molecular beam experiments? The increasingly important role of quantum-chemical calculations in the interpretation of the microwave and NMR data is also highlighted.

Microwave spectroscopy and nuclear magnetic resonance spectroscopy--what is the connection?

The history and development of microwave spectroscopy and nuclear magnetic resonance (NMR) spectroscopy have much in common. In this Account, we discuss the less widely appreciated connections between the parameters measured using the two techniques. Selected examples from our laboratory and from the recent literature attest to the utility and importance of these connections. For example, how are nuclear spin-rotation tensors and NMR chemical shifts related? Why should chemists be interested in absolute magnetic shielding scales? What can chemists learn about trends in spin-spin coupling constants from the hyperfine parameters measured in microwave and molecular beam experiments? The increasingly important role of quantum-chemical calculations in the interpretation of the microwave and NMR data is also highlighted.

Evaluation of the influence of anisotropic indirect nuclear spin-spin coupling tensors on effective residual dipolar couplings for model peptides

Residual dipolar couplings (RDCs) observed between nuclear spins in molecules in partially oriented media have become a valuable source of information for NMR spectroscopists seeking to structurally characterize biological macromolecules. Examination of the form of the direct (D) and indirect (J) nuclear spin-spin coupling Hamiltonians indicates that all observed RDCs contain an unknown contribution from the anisotropic part of J (Delta J) in addition to the direct dipolar contribution, DPQ. Here, we evaluate the influence of DeltaJ on RDCs through a series of DFT calculations on model peptides. Very small corrections to one-bond RDCs measured between heavy atoms in peptides and proteins are recommended: +0.51% for N-C' spin pairs, and +0.45% for C alpha-C' spin pairs. The corrections to RDCs involving at least one proton are negligible. This latter point is likely to be equally applicable to nucleic acids and oligosaccharides in addition to peptides and proteins. Finally, the orientations of the J(N, C') and J(C alpha, C') tensors in the molecular framework are reported for glycylglycine.

Insight into the structure of silver cyanide from (13)C and (15)N solid-state NMR spectroscopy

The structure of silver cyanide has been investigated by solid-state multinuclear magnetic resonance spectroscopy. Carbon-13 and nitrogen-15 NMR spectra of magic-angle-spinning (MAS) and stationary powder samples of isotopically enriched Ag(13)CN, Ag(13)C(15)N, and AgC(15)N have been acquired at the external applied magnetic field strengths 4.7, 7.05, and 9.4 T. Axially symmetric carbon and nitrogen chemical shift (CS) tensors provide evidence for linearity of the polymeric (-Ag-CN-)(n)() chains. A two-site model is required to successfully simulate the (13)C MAS NMR line shape, which is dominated by indirect nuclear spin-spin coupling between (109/107)Ag and (13)C nuclei. In combination with relativistic zeroth-order regular approximation density functional theory (ZORA-DFT) calculations on model AgCN fragments, the (13)C MAS NMR results show that 30 +/- 10% of the silver sites are disordered, that is, either -NC-Ag-CN- or -CN-Ag-NC-, and 70 +/- 10% of the silver sites are ordered, that is, -NC-Ag-NC-. Effective dipolar coupling data extracted from (13)C NMR spectra of stationary samples allow an upper limit of 1.194 A to be placed on the carbon-nitrogen internuclear distance. After incorporation of the effects of anisotropic indirect nuclear spin-spin coupling and motional averaging on the NMR-derived distance, a corrected value of r(CN) = 1.16 +/- 0.03 A is obtained. This work provides an example of the type of information which may be obtained from solid-state NMR studies of disordered materials and how such information may complement that available from diffraction studies.

Interpretation of indirect nuclear spin-spin coupling tensors for polyatomic xenon fluorides and group 17 fluorides: results from relativistic density-functional calculations

Significant improvements have been made recently in the calculation of NMR indirect nuclear spin-spin coupling tensors (J). In particular, the relativistic zeroth-order regular approximation density-functional theory (ZORA-DFT) approach holds great promise for the calculation of spin-spin coupling constants for a variety of chemical systems containing heavy nuclei. In the present work, the ZORA-DFT method is applied to the calculation of the complete reduced coupling tensors, K, for a range of chlorine-, bromine-, iodine-, and xenon-containing species: K(Cl,F) for ClF(2)(+), ClF(3), ClF(4)(+), ClF(5), ClF(6)(-), and ClF(6)(+); K(Br,F) for BrF(3), BrF(6)(-), and BrF(6)(+); K(I,F) for IF(4)(+) and IF(6)(+); K(Xe,F) for XeF(+), XeF(2), XeF(3)(+), XeF(4), XeF(5)(-), XeF(5)(+), and XeF(7)(+). These species represent a wide variety of geometrical bonding arrangements. Agreement between the calculated coupling constants and available experimental data is excellent, and the absolute sign of the coupling constants is provided. It is shown that (1)K(iso) may be positive or negative even within the same molecule, e.g., K(Cl,F)(iso) may be of either sign, depending on the local environment. Periodic trends in (1)K(iso) for isovalent and isostructural molecules are evident. The spin-spin coupling anisotropies, Delta K, and the orientations of the K tensors are also determined. The success of the calculations is a direct result of employing reliable geometries and considering both scalar and spin-orbit relativistic effects. The dependence of K(Cl,F)(iso) and K(Xe,F)(iso) on the local molecular and electronic structure is discussed in terms of the paramagnetic spin-orbit (PSO) and combined Fermi-contact spin-dipolar (FC+SD) coupling mechanisms. The PSO term depends strongly on the number of valence shell electron lone pairs on the central heavy atom, and the FC+SD contribution increases with the Cl[bond]F or Xe[bond]F bond length for a given series of compounds. This interpretation allows for the successful rationalization of the existing experimental data.

Periodic trends in indirect nuclear spin-spin coupling tensors: relativistic density functional calculations for interhalogen diatomics

There have been significant advances in the calculation and interpretation of indirect nuclear spin-spin coupling (J) tensors during the past few years; however, much work remains to be done, especially for molecules containing heavy atoms where relativistic effects may play an important role. Many J tensors cannot be explained based solely on a nonrelativistic Fermi-contact mechanism. In the present work, the relativistic zeroth-order regular approximation density-functional (ZORA-DFT) implementation for the calculation of J has been applied to the complete series of homonuclear and heteronuclear diatomic halogen molecules: F(2), Cl(2), Br(2), I(2), At(2), ClF, BrF, IF, ClBr, ClI, and BrI. For all of these compounds, the reduced isotropic coupling constant (K(iso)) is positive and the reduced anisotropic coupling constant (DeltaK) is negative. With the exception of molecular fluorine, the magnitudes of K(iso) and DeltaK are shown to increase linearly with the product of the atomic numbers of the coupled nuclei. ZORA-DFT calculations of J for F(2) and ClF are in excellent agreement with the results obtained from multiconfigurational self-consistent-field calculations. The relative importance of the various coupling mechanisms is approximately constant for all of the compounds, with the paramagnetic spin-orbit term being the dominant contributor to K(iso), at approximately 70-80%. Available experimental stimulated resonant Raman spectroscopy data are exploited to extract the complete J((127)I,(127)I) tensor for iodine in two rotational states. The dependence of K(iso) and DeltaK on bond length and rovibrational state is investigated by using calculated results in combination with available experimental data. In addition to providing new insights into periodic trends for J coupling tensors, this work further demonstrates the utility of the ZORA-DFT method and emphasizes the necessity of spin-orbit relativistic corrections for J calculations involving heavy nuclei.

Modeling 2hJiso(N, N) in nucleic acid base pairs: ab initio characterization of the 2hJ(N, N) tensor in the methyleneimine dimer as a function of hydrogen bond geometry

The observation of 2hJiso(N, N) coupling has prompted considerable interest in this phenomenon from experimentalists and theoreticians due to the potential these couplings hold for the determination of secondary and tertiary structure in biologically important molecules. Here, we present an ab initio (MCSCF) study of the complete 2hJ(N, N) tensor for a model methyleneimine dimer system as a function of (i) the N-N separation, rNN, and (ii) the hydrogen bond angle, theta. This simple system models the 2hJ(N, N) tensor of nucleic acid base pairs. Results indicate that although the Fermi-contact mechanism dominates 2hJiso(N, N), the coupling tensor is anisotropic due to contributions from the Fermi-contact spin-dipolar cross term. The variation in 2hJiso(N, N) as a function of rNN is fit to an exponential decay. The influence of theta on the coupling constant is less pronounced but must be considered if experimental coupling constants are to be used for quantitative structure determination. Our results for this simple model system demonstrate that 2hJiso(N, N) is a valuable probe of hydrogen bonding in nucleic acid base pairs.

Hyperfine Structure in the Rotational Spectrum of GaF: A Comparison of Experimental and Calculated Spin-Rotation and Electric Field Gradient Tensors

The high-resolution pure rotational spectrum of GaF has been measured using a Balle-Flygare-type Fourier transform spectrometer. Improved nuclear quadrupolar coupling constants and rotational constants have been obtained along with the first reported fluorine spin-rotation constant for gallium fluoride, C(I) ((69)Ga(19)F, v = 0) = +32.0(21) kHz. Accurate spin-rotation tensors from microwave or molecular beam spectroscopy are particularly important to NMR spectroscopists and theoreticians because these data provide information about anisotropic nuclear magnetic shielding in the absence of intermolecular effects. For quadrupolar nuclei such as gallium, the quadrupolar interaction is sufficiently large that it is very difficult to characterize shielding tensors directly via NMR spectroscopy. The experimentally determined nuclear quadrupolar coupling constants and spin-rotation constants for GaF are compared with the results of a series of high-level ab initio calculations carried out at various levels of theory with a range of basis sets. Further calculations on BF and AlF, supplemented with available experimental data for InF and TlF, allow for the investigation of trends in nuclear magnetic shielding, spin-rotation, and electric field gradient tensors in the group-13 fluorides. Calculations at the MP2/6-311++G** and MP2/6-311G(2df, 2pd) levels provide the most consistently satisfactory results in comparison with the experimental data. Copyright 2000 Academic Press.