Some quantum chemical aspects of solvent effects on NMR parameters

Allosteric and dynamic control of RNA-dependent RNA polymerase function and fidelity

All RNA viruses encode an RNA-dependent RNA polymerase (RdRp) responsible for genome replication. It is now recognized that enzymes in general, and RdRps specifically, are dynamic macromolecular machines such that their moving parts, including active site loops, play direct functional roles. While X-ray crystallography has provided deep insight into structural elements important for RdRp function, this methodology generally provides only static snapshots, and so is limited in its ability to report on dynamic fluctuations away from the lowest energy conformation. Nuclear magnetic resonance (NMR), molecular dynamics (MD) simulations and other biophysical techniques have brought new insight into RdRp function by their ability to characterize the trajectories, kinetics and thermodynamics of conformational motions. In particular, these methodologies have identified coordinated motions among conserved structural motifs necessary for nucleotide selection and incorporation. Disruption of these motions through amino acid substitutions or inhibitor binding impairs RdRp function. Understanding and re-engineering these motions thus provides exciting new avenues for anti-viral strategies. This chapter outlines the basics of these methodologies, summarizes the dynamic motions observed in different RdRps important for nucleotide selection and incorporation, and illustrates how this information can be leveraged towards rational vaccine strain development and anti-viral drug design.

Quantum chemical calculations of 77 Se and 125 Te nuclear magnetic resonance spectral parameters and their structural applications

An accurate quantum chemical (QC) modeling of ⁷⁷ Se and ¹²⁵ Te nuclear magnetic resonance (NMR) spectra is deeply involved in the NMR structural assignment for selenium and tellurium compounds that are of utmost importance both in organic and inorganic chemistry nowadays due to their huge application potential in many fields, like biology, medicine, and metallurgy. The main interest of this review is focused on the progress in QC computations of ⁷⁷ Se and ¹²⁵ Te NMR chemical shifts and indirect spin-spin coupling constants involving these nuclei. Different computational methodologies that have been used to simulate the NMR spectra of selenium and tellurium compounds since the middle of the 1990s are discussed with a strong emphasis on their accuracy. A special accent is placed on the calculations resorting to the relativistic methodologies, because taking into account the relativistic effects appreciably influences the precision of NMR calculations of selenium and, especially, tellurium compounds. Stereochemical applications of quantum chemical calculations of ⁷⁷ Se and ¹²⁵ Te NMR parameters are discussed so as to exemplify the importance of integrated approach of experimental and computational NMR techniques.

Structural trends of 77Se-1H spin-spin coupling constants and conformational behavior of 2-substituted selenophenes

Experimental measurements and second-order polarization propagator approach (SOPPA) calculations of (77)Se-(1)H spin-spin coupling constants together with theoretical energy-based conformational analysis in the series of 2-substituted selenophenes have been carried out. A new basis set optimized for the calculation of (77)Se-(1)H spin-spin coupling constants has been introduced by extending the aug-cc-pVTZ-J basis for selenium. Most of the spin-spin coupling constants under study, especially vicinal (77)Se-(1)H couplings, demonstrated a remarkable stereochemical behavior with respect to the internal rotation of the substituent in the 2-position of the selenophene ring, which is of major importance in the stereochemical studies of the related organoselenium compounds.

An estimate of the spin–spin coupling constant, 1J(1H,13C), in gaseous benzene

An excellent linear correlation (r = 0.9999) exists between the spin–spin coupling constants 1J(1H,13C), in benzene dissolved in four solvents (R. Laatikainen et al. J. Am. Chem. Soc. 117, 11006 (1995)) and Ando's solvation dielectric function, ε/(ε – 1). The solvents are cyclohexane, carbon disulfide, pyridine, and acetone. 1J(1H,13C)for gaseous benzene is predicted to be 156.99(2) Hz at 300 K. Key words: spin–spin coupling constants, 1J(1H,13C) for benzene in the vapor phase; spin–spin coupling constants, solvent dielectric constant dependence of 1J(1H,13C) in benzene; benzene, estimate of 1J(1H,13C) in the vapor; nuclear magnetic resonance, estimate of 1J(1H,13C) in gaseous benzene.

One-bond carbon-proton coupling constants: angular dependence in alpha-linked oligosaccharides

An investigation is presented of the angular dependence of 1JC,H in model compounds related to alpha-linked oligosaccharides. Values calculated by FPT formulation in the semi-empirical INDO method for models of (1----1)-, (1----2)-, (1----3)-, and (1----4)-linked disaccharides were compared, and the effect of the orientation of HO-2 was elucidated. The angular dependence of 1JC,H on the glycosidic dihedral angles phi H and psi H was characterised in the form 1JC,H = A cos 2 phi + B cos phi + C sin 2 phi + D sin phi + E. The 1JC,H values, measured by DEPT methods for C-1-H-1 and C-X'-H-X' in various rigid carbohydrates, were used to adjust the calculated angular dependences and to determine solvent effects. Based on the abundance of the conformers for maltose and isomaltose, the thermodynamically averaged 1JC,H values have been calculated. The results obtained (less than 1JC-1,H-1 greater than 169.9, less than 1JC-4',H-4' greater than 147.7 Hz for methyl beta-maltoside and less than 1JC-1,H-1 greater than 169.8 Hz for methyl beta-isomaltoside) agree with the experimental values of 172.4, 147.7, and 170.3 Hz, respectively.