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Ad Bax - One of the best experts on this subject based on the ideXlab platform.
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magnetic field induced residual dipolar couplings of imino groups in nucleic acids from measurements at a single magnetic field
Journal of Biomolecular NMR, 2007Co-Authors: Jinfa Ying, Alexander Grishaev, Michael P Latham, Arthur Pardi, Ad BaxAbstract:For base-paired nucleic acids, variations in (1) J (NH) and the imino (1)H chemical shift are both dominated by Hydrogen Bond Length. In the absence of molecular alignment, the (1) J (NH) coupling for the imino proton then can be approximated by (1) J (NH) = (1.21Hz/ppm)delta(H) - 103.5 +/- 0.6 Hz, where delta(H) represents the chemical shift of the imino proton in ppm. This relation permits imino residual dipolar couplings (RDCs) resulting from magnetic susceptibility anisotropy (MSA) to be extracted from measurement of ((1) J (NH) + RDC) splittings at a single magnetic field strength. Magnetic field-induced RDCs were measured for tRNA(Val) and the alignment tensor determined from magnetic-field alignment of tRNA(Val) agrees well with the tensor calculated by summation of the MSA tensors of the individual nucleobases.
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correlation between 3hjnc and Hydrogen Bond Length in proteins
Journal of the American Chemical Society, 1999Co-Authors: Gabriel Cornilescu, Benjamin E Ramirez, Kirsten M Frank, Marius G Clore, And Angela M Gronenborn, Ad BaxAbstract:Establishing a quantitative relationship between backbone−backbone Hydrogen-Bond (H-Bond) Length observed in protein crystal structures and recently observed 3hJNC‘ couplings across such Bonds is limited by the coordinate precision of the X-ray structure. For an immunoglobulin binding domain of streptococcal protein G, very high-resolution X-ray structures are available. It is demonstrated that over the small range of N−O H-Bond Lengths (2.8−3.3 A) for which 3hJNC‘ couplings are observable, the 32 measured 3hJNC‘ values can be fit to: 3hJNC‘ = −59000 exp(−4RNO) ± 0.09 Hz, or RNO = 2.75 − 0.25 ln(−3hJNC‘) ± 0.06 A. Backbone amide to side-chain carboxyl Hydrogen Bonds were also investigated, and the measured 3hJNC‘ values tend to be smaller than expected from their crystallographically determined H-Bond Lengths. The sign of 3hJNC‘, determined from a zero-quantum/double-quantum experiment, is found to be the same as that of the 1JNH coupling, i.e., negative.
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solution nmr measurement of amide proton chemical shift anisotropy in 15n enriched proteins correlation with Hydrogen Bond Length
Journal of the American Chemical Society, 1997Co-Authors: Nico Tjandra, Ad BaxAbstract:Cross-correlation between 15N−1H dipolar interactions and 1HN chemical shift anisotropy (CSA) gives rise to different relaxation rates of the doublet components of 1H−{15N} peptide backbone amides....
Nico Tjandra - One of the best experts on this subject based on the ideXlab platform.
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solution nmr measurement of amide proton chemical shift anisotropy in 15n enriched proteins correlation with Hydrogen Bond Length
Journal of the American Chemical Society, 1997Co-Authors: Nico TjandraAbstract:Cross-correlation between 15N−1H dipolar interactions and 1HN chemical shift anisotropy (CSA) gives rise to different relaxation rates of the doublet components of 1H−{15N} peptide backbone amides. Two schemes for quantitative measurement of this effect are described and demonstrated for samples of uniformly 15N-enriched ubiquitin and perdeuterated 15N-enriched HIV-1 protease. The degree of relaxation interference correlates with the isotropic 1HN chemical shift, and results indicate that an upfield change of the most shielded principal components of the CSA tensor is correlated with an approximately 2-fold larger downfield shift of the average of the other two components. The magnitude of the relaxation interference is large in β-sheet and considerably smaller in α-helices. This correlation is not dominated by the backbone geometry but reflects the slightly longer Hydrogen Bond Length in helices compared to β-sheet. The smallest relaxation interference effect in ubiquitin is observed for Ser20-HN and Ile...
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solution nmr measurement of amide proton chemical shift anisotropy in 15n enriched proteins correlation with Hydrogen Bond Length
Journal of the American Chemical Society, 1997Co-Authors: Nico Tjandra, Ad BaxAbstract:Cross-correlation between 15N−1H dipolar interactions and 1HN chemical shift anisotropy (CSA) gives rise to different relaxation rates of the doublet components of 1H−{15N} peptide backbone amides....
Isao Ando - One of the best experts on this subject based on the ideXlab platform.
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the amide proton nmr chemical shift and Hydrogen Bonded structure of peptides and polypeptides in the solid state as studied by high frequency solid state 1h nmr
Chemical Physics Letters, 2000Co-Authors: Kazuo Yamauchi, Shigeki Kuroki, Kazuma Fujii, Isao AndoAbstract:Abstract High-resolution 1 H NMR spectra of glycine (Gly)-containing peptides and polypeptides in the solid state were measured at 800 MHz and at high-speed magic-angle-spinning (MAS) of 30 kHz to elucidate the relationship between the Hydrogen-Bond Length and 1 H NMR chemical shift to add to our previous experimental and theoretical findings that there is a relationship between the Hydrogen-Bond Length and 13 C , 15 N and 17 O chemical shifts of various kinds of amino acid residues of peptides and polypeptides in the solid state. From these experimental results, it is found that the 1 H chemical shifts of Gly amide protons of Gly-containing peptides and polypeptides, for which the Hydrogen-Bond Length between the nitrogen and oxygen atoms (RN…O) have already been determined by X-ray diffraction, move downfield with a decrease in RN…O. Theoretical calculations qualitatively explain these experimental results.
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Hydrogen Bonding structural study of solid peptides and polypeptides containing a glycine residue by 17o nmr spectroscopy
Journal of Molecular Structure, 1994Co-Authors: Shigeki Kuroki, Isao Ando, Akira Shoji, Akihiro Takahashi, Takuo OzakiAbstract:Abstract Static 17 O NMR spectra of polyglycines I and II and glycylglycine peptides in the solid state were measured by the cross polarization technique. By computer simulations of these spectra, three NMR parameters (quadrupolar coupling constant ( e 2 qQ / h ), electric field gradient asymmetry parameter (η Q ), and chemical shift (δ)) were determined. From these results, it was found that as the Hydrogen Bond Length decreased, the e 2 qQ / h value decreased. Furthermore, the principal values of the 17 O chemical shift tensor for both the peptides and polypeptides moved upfield with a decrease in the Hydrogen Bond Length. From these experimental findings, it was clarified that 17 O NMR spectroscopy can provide a useful means of elucidating the Hydrogen-Bonding structure in solid peptides and polypeptides.
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Hydrogen Bond Length and 15N NMR chemical shift of the glycine residue of some oligopeptides in the solid state
Journal of Molecular Structure, 1991Co-Authors: Shigeki Kuroki, Naoki Asakawa, Shinji Ando, Isao Ando, Akira Shoji, Takuo OzakiAbstract:Abstract CP-MAS and CP-static 15 N NMR spectra were measured for a variety of solid oligopeptides containing the glycine residue, the crystal structures of which had already been determined by X-ray diffraction. From the results of the observed 15 N chemical shifts, it was found that the isotropic 15 N chemical shifts (σ iso ) of the glycine residues move downfield with a decrease of Hydrogen Bond Lengths ( R N⋯O ) between the nitrogen and oxygen atoms in the amide groups, and that the pricipal value of σ 33 moves linearly downfield with a decrease of R N⋯O . There is no relationship between the principal value of σ 11 or σ 22 and R N⋯O . This indicates that such a linear downfield shift of σ 33 contributes predominantly to the downfield shift σ iso . Quantum chemical calculations of the 15 N shielding constant for the model compounds were carried out by the FPT-INDO method, and the relationship between 15 N chemical shift and R N⋯O discussed.
Gerrit Groenhof - One of the best experts on this subject based on the ideXlab platform.
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the low barrier Hydrogen Bond in the photoactive yellow protein a vacuum artifact absent in the crystal and solution
Journal of the American Chemical Society, 2016Co-Authors: Timo Graen, Ludger Inhester, Maike Clemens, Helmut Grubmuller, Gerrit GroenhofAbstract:There has been considerable debate on the existence of a low-barrier Hydrogen Bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. (Proc. Natl. Acad. Sci., U. S. A., 2009, 106, 440−444) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased Hydrogen Bond Length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large 1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 Hydrogen b...
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The Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution
2016Co-Authors: Timo Graen, Ludger Inhester, Maike Clemens, Helmut Grubmüller, Gerrit GroenhofAbstract:There has been considerable debate on the existence of a low-barrier Hydrogen Bond (LBHB) in the photoactive yellow protein (PYP). The debate was initially triggered by the neutron diffraction study of Yamaguchi et al. (Proc. Natl. Acad. Sci., U. S. A., 2009, 106, 440−444) who suggested a model in which a neutral Arg52 residue triggers the formation of the LBHB in PYP. Here, we present an alternative model that is consistent within the error margins of the Yamaguchi structure factors. The model explains an increased Hydrogen Bond Length without nuclear quantum effects and for a protonated Arg52. We tested both models by calculations under crystal, solution, and vacuum conditions. Contrary to the common assumption in the field, we found that a single PYP in vacuum does not provide an accurate description of the crystal conditions but instead introduces strong artifacts, which favor a LBHB and a large 1H NMR chemical shift. Our model of the crystal environment was found to stabilize the two Arg52 Hydrogen Bonds and crystal water positions for the protonated Arg52 residue in free MD simulations and predicted an Arg52 pKa upshift with respect to PYP in solution. The crystal and solution environments resulted in almost identical 1H chemical shifts that agree with NMR solution data. We also calculated the effect of the Arg52 protonation state on the LBHB in 3D nuclear equilibrium density calculations. Only the charged crystal structure in vacuum supports a LBHB if Arg52 is neutral in PYP at the previously reported level of theory (J. Am. Chem. Soc., 2014, 136, 3542−3552). We attribute the anomalies in the interpretation of the neutron data to a shift of the potential minimum, which does not involve nuclear quantum effects and is transferable beyond the Yamaguchi structure
K F Khaled - One of the best experts on this subject based on the ideXlab platform.
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experimental and atomistic simulation studies of corrosion inhibition of copper by a new benzotriazole derivative in acid medium
Electrochimica Acta, 2009Co-Authors: K F KhaledAbstract:Abstract The efficiency of N-(2-thiazolyl)-1H-benzotriazole-1-carbothioamide (TBC) as a non-toxic corrosion inhibitor for copper in 0.5 M HCl has been tested by weight loss and electrochemical techniques. Electrochemical techniques show that TBC is a mixed-type inhibitor and its inhibition mechanism on copper surface is adsorption assisted by H-Bond formation. Impedance measurements show a wide peak presumably given by more than one time constant in the presence of TBC. Also, impedance results show that the values of CPEs (constant phase elements) tend to decrease and both polarization resistance and inhibition efficiency tend to increase with increasing of TBC concentration due to an increase in the electric double layer. Monte Carlo simulations incorporating molecular mechanics and molecular dynamics show that the TBC adsorb on the copper surface firmly through the thiazolyl and carbothioamide groups, the adsorption energy as well as Hydrogen Bond Length have been calculated for both TBC and benzotriazole (BTA) for comparison. Quantum chemical calculations reveal that TBC has higher HOMO, lower LUMO, lower energy gap and lower dipole moment ( μ ) than BTA, which proves that TBC is better copper corrosion inhibitor compared with BTA in 0.5 M HCl.
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monte carlo simulations of corrosion inhibition of mild steel in 0 5 m sulphuric acid by some green corrosion inhibitors
Journal of Solid State Electrochemistry, 2009Co-Authors: K F KhaledAbstract:Atomistic modelling and simulations are becoming increasingly important in the field of corrosion inhibition. New research and development efforts and new possibilities for using computational chemistry in studying the behaviour of corrosion inhibitors on the metal surfaces are introduced. In this study, Monte Carlo simulations technique incorporating molecular mechanics and molecular dynamics were used to simulate the adsorption of methionine derivatives, namely l-methionine, l-methionine sulphoxide and l-methionine sulphone, on iron (110) surface in 0.5 M sulphuric acid. Adsorption energy as well as Hydrogen Bond Length has been calculated. Results show that methionine derivatives have a very good inhibitive effect for corrosion of mild steel in 0.5 M sulphuric acid solution. Tafel polarisation studies have shown that methionine derivatives act as mixed-type inhibitors, and their inhibition mechanism is adsorption assisted by Hydrogen Bond formation. Impedance results indicate that the values of the constant phase element tend to decrease with increasing methionine derivatives concentrations due to the increase in the thickness of the electrical double layer. In addition, both polarisation resistance and inhibition efficiency Ei(%) tend to increase with increasing inhibitors concentrations due to the increase of the surface coverage, i.e., the decrease of the electrochemical active surface area. The quantum mechanical approach may well be able to foretell molecular structures that are better for corrosion inhibition.
