Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

The performance of the SAOP potential for the calculation of NMR chemical shifts was evaluated. SAOP results show considerable improvement with respect to previous potentials, like VWN or BP86, at least for the carbon, nitrogen, oxygen, and fluorine chemical shifts. Furthermore, a few NMR calculations carried out on third period atoms (S, P, and Cl) improved when using the SAOP potential

NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.

Nuclear magnetic resonance chemical shifts with the statistical average of orbital-dependent model potentials in Kohn-Sham density functional theory

The performance of the SAOP potential for the calculation of NMR chemical shifts was evaluated. SAOP results show considerable improvement with respect to previous potentials, like VWN or BP86, at least for the carbon, nitrogen, oxygen, and fluorine chemical shifts. Furthermore, a few NMR calculations carried out on third period atoms (S, P, and Cl) improved when using the SAOP potential

Configuration of stilbene derivatives by (1)H NMR and theoretical calculation of chemical shifts

The direct E/Z configuration assignment of tri- and tetra-substituted stilbenes (and other analogous olefins) when only one of the isomers is available is a quite challenging task. Sometimes, a chemical transformation or some other tedious method is necessary for determination of the double bond substitution pattern. In this paper, we relied on theoretical calculation of chemical shifts as a complementary tool for (1)H NMR determination of the configuration of an alpha-phenylcinnamic acid prepared as a unique isomer by the Perkin reaction. (C) 2010 Elsevier B.V. All rights reserved.

Solid state NMR chemical shifts as an alternative to diffraction data in the determination of SIC polytypic structures

Silicon carbide, which has many polytypic modifications of a very simple and very symmetric structure, is an excellent model system for exploring, the relationship between chemical shift, long-range dipolar shielding, and crystal structure in network solids. A simple McConnell equation treatment of bond anisotropy effects in a poly type predicts chemical shifts for silicon and carbon sites which agree well with the experiment, provided that contributions from bonds up to 100 A are included in the calculation. The calculated chemical shifts depend on three factors: the layer stacking sequence, electrical centre of gravity, and the spacings between silicon and carbon layers. The assignment of peaks to lattice sites is proved possible for three polytypes (6H, 15R, and 3C). The fact that the calculated chemical shifts are very sensitive to layer spacings provides us a potential way to detennine and refine a crystal structure. In this work, the layer spacings of 6H SiC have been calculated and are within X-ray standard deviations. Under this premise, the layer spacings of 15R have been detennined. 29Si and 13C single crystal nmr studies of 6H SiC polytype indicate that all silicons and carbons are magnetically anisotropic. The relationship between a magnetic shielding tensor component and layer spacings has been derived. The comparisons between experimental and semi-empirical chemical shielding tensor components indicate that the paramagnetic shielding of silicon should be included in the single crystal chemical shift calculation.

Pressure Dependence of N-15 Chemical Shifts in Model Peptides Ac-Gly-Gly-X-Ala-NH2

High pressure NMR spectroscopy has developed into an important tool for studying conformational equilibria of proteins in solution. We have studied the amide proton and nitrogen chemical shifts of the 20 canonical amino acids X in the random-coil model peptide Ac-Gly-Gly-X-Ala-NH2, in a pressure range from 0.1 to 200 MPa, at a proton resonance frequency of 800 MHz. The obtained data allowed the determination of first and second order pressure coefficients with high accuracy at 283 K and pH 6.7. The mean first and second order pressure coefficients <B-1(15N)> and <B-2(15N)> for nitrogen are 2.91 ppm/GPa and -2.32 ppm/GPa(2), respectively. The corresponding values <B-1(1H)> and <B-2(1H)> for the amide protons are 0.52 ppm/GPa and -0.41 ppm/GPa(2). Residual dependent (1)J(1H15N)-coupling constants are shown.

Unusual 1H NMR chemical shifts support (His) Cɛ1—H⋅⋅⋅O⩵C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis

13C-selective NMR, combined with inhibitor perturbation experiments, shows that the Cɛ1—H proton of the catalytic histidine in resting α-lytic protease and subtilisin BPN′ resonates, when protonated, at 9.22 ppm and 9.18 ppm, respectively, which is outside the normal range for such protons and ≈0.6 to 0.8 ppm further downfield than previously reported. They also show that the previous α-lytic protease assignments [Markley, J. L., Neves, D. E., Westler, W. M., Ibanez, I. B., Porubcan, M. A. & Baillargeon, M. W. (1980) Front. Protein Chem. 10, 31–61] were to signals from inactive or denatured protein. Simulations of linewidth vs. pH demonstrate that the true signal is more difficult to detect than corresponding signals from inactive derivatives, owing to higher imidazole pKa values and larger chemical shift differences between protonated and neutral forms. A compilation and analysis of available NMR data indicates that the true Cɛ1—H signals from other serine proteases are similarly displaced downfield, with past assignments to more upfield signals probably in error. The downfield displacement of these proton resonances is shown to be consistent with an H-bond involving the histidine Cɛ1—H as donor, confirming the original hypothesis of Derewenda et al. [Derewenda, Z. S., Derewenda, U. & Kobos, P. M. (1994) J. Mol. Biol. 241, 83–93], which was based on an analysis of literature x-ray crystal structures of serine hydrolases. The invariability of this H-bond among enzymes containing Asp-His-Ser triads indicates functional importance. Here, we propose that it enables a reaction-driven imidazole ring flip mechanism, overcoming a major dilemma inherent in all previous mechanisms, namely how these enzymes catalyze both the formation and productive breakdown of tetrahedral intermediates.

NMR of conotoxins: structural features and an analysis of chemical shifts of post-translationally modified amino acids

Conotoxins are small conformationally constrained peptides found in the venom of marine snails of the genus Conus. They are usually cysteine rich and frequently contain a high degree of post-translational modifications such as C-terminal amidation, hydroxylation, carboxylation, bromination, epimerisation and glycosylation. Here we review the role of NMR in determining the three-dimensional structures of conotoxins and also provide a compilation and analysis of H-1 and C-13 chemical shifts of post-translationally modified amino acids and compare them with data from common amino acids. This analysis provides a reference source for chemical shifts of post-translationally modified amino acids. Copyright (C) 2006 John Wiley & Sons, Ltd.

Solvent induced NMR chemical shifts that arise from molecular encounters

Recently Homer and Percival have postulated that intermolecular van der Waals dispersion forces can be characterized by three mechanisms. The first arises via the mean square reaction field < R1; 2> due to the transient dipole of a particular solute molecule that is considered situated in a cavity surrounded by solvent molecules; this was characterized by an extended Onsager approach. The second stems from the extra cavity mean square reaction field < R2; 2> of the near neighbour solvent molecules. The third originates from square field electric fields E2BI due to a newly characterized effect in which solute atoms are `buffeted' by the peripheral atoms of adjacent solvent molecules. The present work concerns more detailed studies of the buffeting screening, which is governed by sterically controlled parameter (2T - T)2, where and are geometric structural parameters. The original approach is used to characterise the buffeting shifts induced by large solvent molecules and the approach is found to be inadequate. Consequently, improved methods of calculating and are reported. Using the improved approach it is shown that buffeting is dependent on the nature of the solvent as well as the nature of the solute molecule. Detailed investigation of the buffeting component of the van der Waals chemical shifts of selected solutes in a range of solvents containing either H or Cl as peripheral atoms have enabled the determination of a theoretical acceptable value for the classical screening coefficient B for protons. 1H and 13C resonance studies of tetraethylmethane and 1H, 13C and 29Si resonance studies of TMS have been used to support the original contention that three (< R1; 2> , < R2; 2> and E2BI) components of intermolecular van der Waals dispersion fields are required to characterise vdW chemical shifts.

A theoretical and experimental study to unequivocal structural assignment of tetrahydroquinoline derivatives

The tetrahydroquinoline derivatives can be easily synthesized through Povarov reaction and have several important biological activities. This work describes a comparative study for the unequivocal assignment of molecular structure of different tetrahydroquinoline derivatives, through a complete analysis of NMR 1D and 2D NMR spectra (1H, 13C, COSY, HSQC, and HMBC), and the correlation this data with theoretical calculations of energy-minimization and chemical shift (δ), employing the theory level of DFT/B3LYP with set of the cc-pVDZ basis. For these derivatives the experimental analyses and the theoretical model adopted were sufficient to obtain a good description of its structures, and these results can be used to assign the structure of various others tetrahydroquinoline derivatives. © 2013 Springer Science+Business Media New York.

Synthetic scope and DFT analysis of the chiral binap-gold (I) complex-catalyzed 1,3-dipolar cycloaddition of azlactones with alkenes

The 1,3-dipolar cycloaddition between glycine-derived azlactones with maleimides is efficiently catalyzed by the dimeric chiral complex [(Sa)-Binap·AuTFA]2. The alanine-derived oxazolone only reacts with tert-butyl acrylate giving anomalous regiochemistry, which is explained and supported by Natural Resonance Theory and Nucleus Independent Chemical Shifts calculations. The origin of the high enantiodiscrimination observed with maleimides and tert-butyl acrylate is analyzed using DFT computed at M06/Lanl2dz//ONIOM(b3lyp/Lanl2dz:UFF) level. Several applications of these cycloadducts in the synthesis of new proline derivatives with a 2,5-trans-arrangement and in the preparation of complex fused polycyclic molecules are described.