Unusual long-range spin-spin coupling in fluorinated polyenes: a mechanistic analysis

Nuclear magnetic resonance (NMR) is a prospective means to realize quantum computers. The performance of a NMR quantum computer depends sensitively on the properties of the NMR-active molecule used, where one requirement is a large indirect spin-spin coupling over large distances. F-F spin-spin coupling constants (SSCCs) for fluorinated polyenes F-(CH==CH)n-F (n=1cdots, three dots, centered5) are >9 Hz across distances of more than 10 A. Analysis of the F,F spin-spin coupling mechanism with our recently developed decomposition of J into Orbital Contributions with the help of Orbital Currents and Partial Spin Polarization (J-OCOC-PSP=J-OC-PSP) method reveals that coupling is dominated by the spin-dipole (SD) term due to an interplay between the pi lone-pair orbitals at the F atoms and the pi(C2n) electron system. From our investigations we conclude that SD-dominated SSCCs should occur commonly in molecules with a contiguous pi-electron system between the two coupling nuclei and that a large SD coupling generally is the most prospective way to provide large long-range spin-spin coupling. Our results give guidelines for the design of suitable active molecules for NMR quantum computers.     

Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids

Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.     

The calculation of indirect nuclear spin-spin coupling constants in large molecules

We present calculations of indirect nuclear spin-spin coupling constants in large molecular systems, performed using density functional theory. Such calculations, which have become possible because of the use of linear-scaling techniques in the evaluation of the Coulomb and exchange-correlation contributions to the electronic energy, allow us to study indirect spin-spin couplings in molecules of biological interest, without having to construct artificial model systems. In addition to presenting a statistical analysis of the large number of short-range coupling constants in large molecular systems, we analyse the asymptotic dependence of the indirect nuclear spin-spin coupling constants on the internuclear separation. In particular, we demonstrate that, in a sufficiently large one-electron basis set, the indirect spin-spin coupling constants become proportional to the inverse cube of the internuclear separation, even though the diamagnetic and paramagnetic spin-orbit contributions to the spin-spin coupling constants separately decay as the inverse square of this separation. By contrast, the triplet Fermi contact and spin-dipole contributions to the indirect spin-spin coupling constants decay exponentially and as the inverse cube of the internuclear separation, respectively. Thus, whereas short-range indirect spin-spin coupling constants are usually dominated by the Fermi contact contribution, long-range coupling constants are always dominated by the negative diamagnetic spin-orbit contribution and by the positive paramagnetic spin-orbit contribution, with small spin-dipole and negligible Fermi contact contributions.     

Methodological aspects in the calculation of parity-violating effects in nuclear magnetic resonance parameters

We examine the quantum chemical calculation of parity-violating (PV) electroweak contributions to the spectral parameters of nuclear magnetic resonance (NMR) from a methodological point of view. Nuclear magnetic shielding and indirect spin-spin coupling constants are considered and evaluated for three chiral molecules, H2O2, H2S2, and H2Se2. The effects of the choice of a one-particle basis set and the treatment of electron correlation, as well as the effects of special relativity, are studied. All of them are found to be relevant. The basis-set dependence is very pronounced, especially at the electron correlated ab initio levels of theory. Coupled-cluster and density-functional theory (DFT) results for PV contributions differ significantly from the Hartree-Fock data. DFT overestimates the PV effects, particularly with nonhybrid exchange-correlation functionals. Beginning from third-row elements, special relativity is of importance for the PV NMR properties, shown here by comparing perturbational one-component and various four-component calculations. In contrast to what is found for nuclear magnetic shielding, the choice of the model for nuclear charge distribution--point charge or extended (Gaussian)--has a significant impact on the PV contribution to the spin-spin coupling constants.     

1H (1-D and 2-D) NMR spectra and the conformational states of some 3-monosubstituted saturated five-membered heterocycles

We have recorded the¹H (1-D and 2-D) NMR spectra of sulfolane, a series of 3-monosubstituted sulfolanes, and 3-acetoxy-1,1-diphenylsilacyclopentane. We have determined the chemical shifts and the proton-proton spin-spin coupling constants of seven ring protons. From analysis of the magnitudes of the vicinal spin-spin coupling constants and consideration of the full-cycle pseudorotation model for five-membered heterocycles, we found that seven conformers are most probable for 3-iodo- and 3-tert-butylsulfolanes. Four of these conformers have the half-chair conformation, three have the envelope conformation with pseudoequatorial substituents. The rest of the 3-monosubstituted sulfolanes (chloro-, bromo-, hydroxy-, and methacryloxysulfolanes) and 3-acetoxy-1,1-diphenylsilacyclopentane also have seven preferred conformations, but with pseudoaxial substituents.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 9, pp. 2035–2040, September, 1991.     

Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.     

Assessment of a Coulomb-attenuated exchange-correlation energy functional

The recently proposed CAM-B3LYP exchange-correlation energy functional, based on a partitioning of the r operator in the exchange interaction into long- and short-range components, is assessed for the determination of molecular thermochemistry, structures, and second order response properties. Rydberg and charge transfer excitation energies and static electronic polarisabilities are notably improved over the standard B3LYP functional; classical reaction barriers also improve. Ionisation potentials, bond lengths, NMR shielding constants and indirect spin-spin coupling constants are comparable with the two functionals. CAM-B3LYP atomisation energies and diatomic harmonic vibrational wavenumbers are less accurate than those of B3LYP. Future research directions are outlined.     

Vibrational contributions to indirect spin-spin coupling constants calculated via variational anharmonic approaches

Zero-point vibrational contributions to indirect spin-spin coupling constants for N2, CO, HF, H2O, C2H2, and CH4 are calculated via explicitly anharmonic approaches. Thermal averages of indirect spin-spin coupling constants are calculated for the same set of molecules and for C2X4, X = H, F, Cl. Potential energy surfaces have been calculated on a grid of points and analytic representations have been obtained by a linear least-squares fit in a direct product polynomial basis. Property surfaces have been represented by a fourth-order Taylor expansion around the equilibrium geometry. The electronic structure calculations employ density functional theory, and vibrational contributions to indirect spin-spin coupling constants are calculated employing vibrational self-consistent-field and vibrational configuration-interaction methods. The performance of vibrational perturbation theory and various approximate variational calculations are discussed. Thermal averages are computed by state-specific and virtual vibrational self-consistent-field methods.     

Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution

In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute-solvent configurations extracted from the MD simulation at 300 K are found to be inferior to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations visited during the molecular dynamics run as well as inaccuracies in geometrical parameters generated from the classical molecular dynamics simulations.     

Additivity of substituent effects on the proton-proton coupling constants of disubstituted pyridines

From the spin-spin coupling constants of pyridine and monosubstituted pyridines the effects of several substituents have been calculated- Assuming an additivity relationship when two of these substituents are present in the same molecule, the spin-spin coupling constants for 11 disubstituted pyridines have been calculated.The NMR spectra of 13 disubstituted pyridines have been studied to obtain accurate values of their coupling constants. The experimental values of these constants are in very good agreement with those calculated using the additivity relationships.     

Theoretical and Experimental Conformational Studies of Oligoglucosides Structurally Related to Fragments of Fungal Cell Wall β-(1→3)-D-Glucan

The conformational behavior of linear oligo-β-(1→3)-D-glucosides was studied using NMR experiments and molecular modeling. The explicit solvent model in calculations yielded the best coincidence between experimental and theoretical values of NOE and spin-spin coupling constants to evidence the strong influence of solvation upon the conformations of the oligoglucosides. Long-range coupling constants calculated for di- and trimeric clusters of the studied glucosides fit the experimental data much better than the single-molecule approach. It was shown that conformational properties of disaccharide fragments in studied oligoglucosides depended on neither their position in the chain nor the length of the chain.     

Predicting the NMR spectra of nucleotides by DFT calculations: cyclic uridine monophosphate

We present an experimental and quantum chemical NMR study of the mononucleotide cyclic uridine monophosphate in water. Spectral parameters ((1)H and (13)C chemical shifts and (1)H--(1)H, (13)C--(1)H, (31)P--(13)C and (31)P--(1)H spin-spin coupling constants) have been carefully obtained experimentally and calculated using DFT methods including the solvent effect and the conformational flexibility of the solute. This study confirms that the (1)H and (13)C spectra of polar, flexible molecules in aqueous solution can be predicted with a high level of accuracy, comparable to that obtained for less complex systems.     

Intramolecular hydrogen bonding in disubstituted ethanes: general considerations and methodology in quantum mechanical calculations of the conformational equilibria of succinamate monoanion

The importance of intramolecular hydrogen bonding between the carboxylate oxygen and amide proton of succinamate anion has been investigated by quantum mechanical simulations as a function of solvent for comparison with conformational equilibria estimated by NMR spectroscopy. The focus is on those methodological considerations of general interest to the conformational equilibrium problem, which are also particularly relevant to the quantum calculations. The roughly planar symmetry of the amide and carboxylate substituents of succinamate anion and the possibility of intramolecular hydrogen-bond formation together suggest that the orientational degrees of freedom of the substituents could play an important role in the equilibrium of the CH2-CH2 torsion. To test this hypothesis, two-dimensional potential-energy surfaces (PESs) were mapped out from the quantum mechanical calculations, with coordinates corresponding to the CH2-CH2 torsional and amide group rotational degrees of freedom. The Boltzmann populations obtained from two-dimensional PESs and those obtained from a one-dimensional adiabatic surface for the CH2-CH2 torsion were compared with the experimental results. In these comparisons, the agreement of calculated gauche fractions with corresponding experimental values was checked, as well as the agreement between predicted coupling constants and those determined from experimental spectra. In polar protic and aprotic solvents, where highly polar trans conformations can be stabilized by dipole-dipole and hydrogen-bonding interactions with the solvent, the orientational degree of freedom of the amide substituent appears to play a sufficiently important role in the CH2-CH2 torsional equilibrium that it cannot be safely ignored in the simulations.     

Between Two Chairs: Combination of Theory and Experiment for the Determination of the Conformational Dynamics of Xylosides

The conformational properties of monosaccharides constitute fundamental features of oligosaccharides. While the energy landscape of monosaccharides can be altered by a specific biochemical environment or by chemical modifications, the analysis of resulting dynamic conformational equilibria is not feasible by experimental means alone. In this work, a series of β-d -xylopyranosides is used to outline how a combination of experimental NMR parameters and computed molecular properties can be used to determine conformers and quantify the composition of conformational equilibria. We demonstrate that identifying the most stable conformers using energy calculations is challenging and computing of NMR shieldings is typically not sensitive enough. On the other hand, computed spin-spin coupling constants for the xyloside ring can be used to unambiguously assign experimental NMR data of dynamic conformational equilibria and quantify the ratio of different conformers in the mixture. As a proof of principle, this procedure allowed to analyze a hitherto unknown dynamic equilibrium of a diamino-xyloside as a precursor of a molecular switch.     

Effect of beta-O-glucosylation on L-Ser and L-Thr diamides: a bias toward alpha-helical conformations

Beta-D-O-glucosylation produces a remarkable effect on the peptide backbone of the model peptides derived from serine and threonine. Consequently, this type of glycosylation is responsible for the experimentally observed shift from extended conformations (model peptides) towards the folded conformations (model glycopeptides). The conclusion has been solidly assessed by a combined NMR/MD protocol. Interestingly, the MD (molecular dynamics) results for the glycopeptides point towards the existence of water-bridging molecules between the sugar and peptide moieties, which could explain the stabilization of the folded conformers in aqueous solution.     

Conformation of δ-cadinol in solution

An assignment of the signals in the¹³C and¹H NMR spectra of the natural sesquiterpene alcohol δ-cadinol has been made by the NMR method (INADEQUATE, 2D-INADEQUATE, two-dimensional C-H correlation on¹J_CH constants, two-dimensional homonuclear J-spectroscopy) and the spin-spin coupling constants¹J_CC and some J_HH constants have been determined. By comparing the experimental and calculated values of the spin-spin coupling constants J_HH it has been shown that the predominant conformation of the δ-cadinol molecule in solution is that in which ring A has the half-chair form and ring B the chair form with an equatorial arrangement of the hydroxy and isopropyl groups. Institute of Organic Chemistry, Siberian Branch, Academy of Sciences of the USSR, Novosibirsk. Translated from Khimiya Prirodnykh Soedinenii, No. 5, pp. 635–638, September–October, 1990.     

Conformational and substituent effects in the 19F spectra of C7-C10 straight-chain chlorofluoroalkanes

One- and two-dimensional fluorine NMR spectra of straight-chain chlorofluoroalkanes having 7-10 carbons were obtained and interpreted. Spectral assignments were based primarily on indirect spin-spin correlations. A scale of chlorine substituent effects was developed. The effects of asymmetric CFCl centers on chemical-shift differences in nearby CF2 groups were analyzed in terms of molecular conformational effects. Spin-spin coupling patterns of CF3 groups were elucidated.