scholarly journals Stabilization of N-, N,N-, N,N′-methylated and unsubstituted simple amidine salts by multifurcated hydrogen bonds

2006 ◽  
Vol 20 (4) ◽  
pp. 169-176 ◽  
Author(s):  
Jarosław Spychała
Keyword(s):  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Biological Properties ◽  
Carbonyl Oxygen ◽  
Relative Strength ◽  
Intramolecular Interactions ◽  
Covalent Bonds ◽  
Natural Isotopic Abundance

In the light of the usefulness of amidines in medicinal chemistry, this paper considers the effects on biological properties and chemical reactivities of organic molecules affected by intramolecular interactions. The study of chemical shifts has been an important source of information on the electronic structure of amidine salts and their ability to form non-covalent bonds with nucleic acids. The NMR and IR results demonstrate that hydrogen bonds are a force for promoting chemical reactions. The thymine O2 carbonyl oxygen in a close proximity to the amidinium cation does interact with the appropriately spaced amidinium NH donor moieties. The1H-15N 2D NMR (GHSQC and GHMBC) spectra with natural isotopic abundance of15N fully confirm the intramolecular character of the bonds. A rule able to estimate the relative strength of the new multifurcated hydrogen bonds is given. The appearance of the ΔδNHchemical shift differences near zero is due to the strong intramolecular interactions. The strength of the H-bond donation by acetamidines is reflected in the N–H dissociation/recombination process (positive charge shift has been invoked to explain other effects on benzamidines). The temperature dependence of chemical shift for the amidine NH protons in dimethyl sulfoxide solutions is herein discussed.

scholarly journals Experimental and theoretical charge density of DL-alanyl-methionine

2001 ◽  
Vol 57 (4) ◽  
pp. 567-578 ◽  
Author(s):  
Régis Guillot ◽  
Nicolas Muzet ◽  
Slimane Dahaoui ◽  
Claude Lecomte ◽  
Christian Jelsch
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Carbonyl Oxygen ◽  
Intramolecular Interactions ◽  
Geometrical Parameters ◽  
Covalent Bonds ◽  
Area Detector ◽  
Lone Pairs

X-ray diffraction data up to d = 0.50 Å resolution have been collected at 100 K for a DL-alanyl-methionine single crystal using a CCD area detector. Multipolar crystallographic refinement was carried out and the electron density of the molecule has been analyzed. The deformation electron density around the S atom reveals two lone pairs with an sp 3 hybridization and agrees with the results of density functional theory calculations. The topological properties of the covalent bonds and of the hydrogen bonds have been investigated. Two weak polar intramolecular interactions of the type C5 (pentagonal cyclic structure) have unfavorable geometrical parameters for hydrogen bonds and are devoid of critical points. The two electron lone pairs of the carbonyl oxygen appear asymmetric in the experimental deformation density. This could be attributed to the different strength of the hydrogen bond and intramolecular polar interaction involving the carbonyl oxygen. In the ab-initio-derived deformation maps, the asymmetry of the electron doublets is reproduced only very partially.

scholarly journals H/D Isotope Effects on 1H-NMR Chemical Shifts in Cyclic Heterodimers and Heterotrimers of Phosphinic and Phosphoric Acids

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1907 ◽  
Author(s):  
Valeriia V. Mulloyarova ◽  
Daria O. Ustimchuk ◽  
Aleksander Filarowski ◽  
Peter M. Tolstoy
Keyword(s):  
Chemical Shift ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
1H Nmr ◽  
31P Nmr ◽  
Chemical Shifts ◽  
Isotope Effects ◽  
Proton Chemical Shift ◽  
Steric Factors ◽  
Solvent Formation

Hydrogen-bonded heterocomplexes formed by POOH-containing acids (diphenylphosphoric 1, dimethylphosphoric 2, diphenylphosphinic 3, and dimethylphosphinic 4) are studied by the low-temperature (100 K) 1H-NMR and 31P-NMR using liquefied gases CDF3/CDF2Cl as a solvent. Formation of cyclic dimers and cyclic trimers consisting of molecules of two different acids is confirmed by the analysis of vicinal H/D isotope effects (changes in the bridging proton chemical shift, δH, after the deuteration of a neighboring H-bond). Acids 1 and 4 (or 1 and 3) form heterotrimers with very strong (short) H-bonds (δH ca. 17 ppm). While in the case of all heterotrimers the H-bonds are cyclically arranged head-to-tail, ···O=P–O–H···O=P–O–H···, and thus their cooperative coupling is expected, the signs of vicinal H/D isotope effects indicate an effective anticooperativity, presumably due to steric factors: when one of the H-bonds is elongated upon deuteration, the structure of the heterotrimer adjusts by shortening the neighboring hydrogen bonds. We also demonstrate the formation of cyclic tetramers: in the case of acids 1 and 4 the structure has alternating molecules of 1 and 4 in the cycle, while in case of acids 1 and 3 the cycle has two molecules of 1 followed by two molecules of 3.

scholarly journals Powder Crystallography by Combining NMR and Crystal Structure Predictions

2014 ◽  
Vol 70 (a1) ◽  
pp. C136-C136 ◽  
Author(s):  
Cory Widdifield ◽  
Maria Baias ◽  
Jean-Nicolas Dumez ◽  
Per H. Svensson ◽  
Hugh Thompson ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Chemical Shift ◽  
Structure Determination ◽  
Structure Prediction ◽  
Density Functional ◽  
De Novo ◽  
Chemical Shifts ◽  
2D Nmr ◽  
Other Information ◽  
13C Chemical Shift

State-of-the-art work in the field of NMR crystallography for molecular systems at natural abundance has recently focused on the accurate measurement of 1H chemical shift values. We will show how when coupled with crystal structure prediction (CSP) methods, this protocol is well-suited for solving the crystal structures of small to medium sized organic molecules, including cocaine and the de-novo structure determination of AZD8329.[1,2] As complementary 1D and 2D NMR experiments are needed for the 1H assignment process, other information, such as isotropic 13C chemical shift values (δiso) are measured. Unfortunately, 13C chemical shifts are not generally useful for structure determination. Additional NMR parameters that are sensitive to structure would ensure that the structure determination procedure is robust, and would provide more accurate refinements when studying larger or more challenging systems. Here, we measure 13C chemical shift tensors for a variety of prototypical organic pharmaceuticals and use density functional theory computations under the gauge-including projector augmented-wave (GIPAW) formalism to probe whether these parameters may be discriminatory for unit cell determinations and structure determination (notably when added to the CSP + 1H chemical shifts protocol).

Temperature dependence of chemical shifts of protons in hydrogen bonds. Experimental evidence on an intramolecular hydrogen bond

1968 ◽  
Vol 46 (17) ◽  
pp. 2865-2868 ◽  
Author(s):  
T. Schaefer ◽  
G. Kotowycz
Keyword(s):  
Hydrogen Bond ◽  
Carbon Tetrachloride ◽  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Temperature Dependence ◽  
Intramolecular Hydrogen Bond ◽  
Chemical Shifts ◽  
Hydroxyl Proton ◽  
Intramolecular Hydrogen ◽  
Strong Intramolecular Hydrogen Bond

A temperature dependence of the chemical shift of the hydroxyl proton in the strong intramolecular hydrogen bond in 3,5-dichlorosalicylaldehyde is observed in carbon tetrachloride and benzene-d6 solutions. Its magnitude of 0.25 to 0.30 × 10−2 p.p.m. per ° C over a range of 100 °C is in agreement with the model described by Muller and Reiter (1).

NUCLEAR SHIELDING PARAMETERS FOR PROTONS IN HYDROGEN BONDS: II. CORRELATION OF CHEMICAL SHIFTS IN INTRAMOLECULAR HYDROGEN BONDS WITH INFRARED STRETCHING FREQUENCIES

1960 ◽  
Vol 38 (8) ◽  
pp. 1249-1254 ◽  
Author(s):  
L. W. Reeves ◽  
E. A. Allan ◽  
K. O. Strømme
Keyword(s):  
Hydrogen Bond ◽  
Chemical Shift ◽  
Hydrogen Bonds ◽  
Infinite Dilution ◽  
Chemical Shifts ◽  
Intramolecular Hydrogen Bonds ◽  
A Value ◽  
Nuclear Shielding ◽  
Intramolecular Hydrogen ◽  
Hydrogen Bonded

Nuclear shielding parameters have been obtained for 24 intramolecularly hydrogen-bonded phenols and naphthols. The shielding parameters are corrected for large diamagnetic anisotropies and a value ΔσOH obtained which represents the change in shielding parameter in parts per million with reference to the infinite dilution chemical shift of phenol, α-naphthol, or β-naphthol. These values of ΔσOH are approximately proportional to the change ΔvOH in the OH stretching frequency on formation of the hydrogen bond.

scholarly journals Oxygenated Theonellastrols: Interpretation of Unusual Chemical Behaviors Using Quantum Mechanical Calculations and Stereochemical Reassignment of 7α-Hydroxytheonellasterol

Marine Drugs ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. 607
Author(s):  
A-Young Shin ◽  
Hyi-Seung Lee ◽  
Yeon-Ju Lee ◽  
Jong Seok Lee ◽  
Arang Son ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Atomic Orbital ◽  
2D Nmr ◽  
Quantum Mechanical ◽  
Quantum Mechanical Calculations ◽  
Epoxy Alcohol ◽  
Theonella Swinhoei ◽  
Nmr Data ◽  
Chemical Shift Calculations

A total of eight new oxygenated 4-exo-methylene sterols, 1–8, together with one artifact 9 and six known sterols 11–16, were isolated from the marine sponge Theonella swinhoei collected from the Bohol province in Philippines. Structures of sterols 1–8 were determined from 1D and 2D NMR data. Among the sterols, 8α-hydroxytheonellasterol (4) spontaneously underwent an allylic 1,3-hydroxyl shift to produce 15α-hydroxytheonellasterol (9) as an artifact; this was rationalized by quantum mechanical calculations of the transition state. In addition, the 1,2-epoxy alcohol subunit of 8α-hydroxy-14,15-β-epoxytheonellasterol (5) was assigned using the Gauge-Independent Atomic Orbital (GIAO) NMR chemical shift calculations and subsequent DP4+ analysis. Finally, comparison of the 13C chemical shifts of isolated 7α-hydroxytheonellasterol (6) with the reported values revealed significant discrepancies at C-6, C-7, C-8, and C-14, leading to reassignment of the C-7 stereochemistry in the known structure.

scholarly journals Carbon Atoms Speaking Out: How the Geometric Sensitivity of 13C Chemical Shifts Leads to Understanding the Colour Tuning of Phycocyanobilin in Cph1 and AnPixJ

Molecules ◽  
2020 ◽  
Vol 25 (23) ◽  
pp. 5505
Author(s):  
Sascha Jähnigen ◽  
Daniel Sebastiani
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Explanatory Power ◽  
Nmr Chemical Shift ◽  
Correlation Pattern ◽  
Covalent Bonds ◽  
Absorption Frequency ◽  
13C Chemical Shifts ◽  
Nmr Chemical Shifts ◽  
Colour Tuning

We present a combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics–statistical approach for the interpretation of nuclear magnetic resonance (NMR) chemical shift patterns in phycocyanobilin (PCB). These were originally associated with colour tuning upon photoproduct formation in red/green-absorbing cyanobacteriochrome AnPixJg2 and red/far-red-absorbing phytochrome Cph1Δ2. We pursue an indirect approach without computation of the absorption frequencies since the molecular geometry of cofactor and protein are not accurately known. Instead, we resort to a heuristic determination of the conjugation length in PCB through the experimental NMR chemical shift patterns, supported by quantum chemical calculations. We have found a characteristic correlation pattern of 13C chemical shifts to specific bond orders within the π-conjugated system, which rests on the relative position of carbon atoms with respect to electron-withdrawing groups and the polarisation of covalent bonds. We propose the inversion of this regioselective relationship using multivariate statistics and to apply it to the known experimental NMR chemical shifts in order to predict changes in the bond alternation pattern. Therefrom the extent of electronic conjugation, and eventually the change in absorption frequency, can be derived. In the process, the consultation of explicit mesomeric formulae plays an important role to qualitatively account for possible conjugation scenarios of the chromophore. While we are able to consistently associate the NMR chemical shifts with hypsochromic and bathochromic shifts in the Pg and Pfr, our approach represents an alternative method to increase the explanatory power of NMR spectroscopic data in proteins.

Reactions of hydroxamidovanadate with peptides: Aqueous equilibria and crystal structure of oxobis(hydroxamido)-glycylglycinatovanadium(V)

1997 ◽  
Vol 75 (2) ◽  
pp. 183-191 ◽  
Author(s):  
Pradip C. Paul ◽  
Sarah J. Angus-Dunne ◽  
Raymond J. Batchelor ◽  
Frederick W.B. Einstein ◽  
Alan S. Tracey
Keyword(s):  
Crystal Structure ◽  
Chemical Shift ◽  
Formation Constant ◽  
Chemical Shifts ◽  
Carbonyl Oxygen ◽  
Monoclinic Space Group ◽  
Coordination Geometry ◽  
Apical Position ◽  
Space Group ◽  
Monomeric Complex

Bis(hydroxamido)hydroxooxovanadate has been found to undergo favourable condensation reactions with simple peptides such as glycylglycine, glycylglycylglycine, or glycyltyrosine to afford, in each case, three products in the approximate ratio 1:3.5:0.2. The three products had the same ligand stoichiometry and, in the case of glycylglycine, an overall formation constant of 3.3 × 103 M−1 for the addition of GlyGly to bis(hydroxamido)vanadate. The 51V chemical shift range of the products (close to −850 ppm) overlaps that of the starting complexes and the products may well have a coordination geometry similar to the parent complexes. The chemical shifts observed for these materials are in the range of chemical shifts observed for peroxovanadium complexes. A crystalline monomeric complex with a single glycylglycinato ligand was obtained and its crystal structure determined. The complex is zwitterionic and has a pentagonal bipyramidal coordination at vanadium with the glycine-NH2 functionality coordinated in the plane of the two hydroxyalamine ligands and the amido carbonyl oxygen in the apical position. Some comparisons with peroxovanadium complexes are drawn. Crystal structure of V(O)(ONH2)2(GlyGly)•H2O: monoclinic, space group Cc; Z = 4; a = 9.1340(9) Å; b = 16.3355(15) Å; c = 7.1149(6) Å; β(°) = 103.020(7); V = 1034.31 Å3; T = 295 K; RF = 0.21 for 2513 data (I0 ≥ 2.5σ(I0)) and 197 variables. Keywords: vanadate, hydroxylamine, N-methylhydroxylamine, oxobis(hydroxamido)glycylglycinatovanadium(V), peptide complex, glycylglycine, 51V NMR, crystal structure.

scholarly journals Secondary structure of hyaluronate in solution. A 1H-n.m.r. investigation at 300 and 500 MHz in [2H6]dimethyl sulphoxide solution

1984 ◽  
Vol 220 (1) ◽  
pp. 197-205 ◽  
Author(s):  
J E Scott ◽  
F Heatley ◽  
W E Hull
Keyword(s):  
Secondary Structure ◽  
Hydrogen Bonds ◽  
Oxygen Atom ◽  
Glucuronic Acid ◽  
Chondroitin Sulphate ◽  
Chemical Shifts ◽  
Heparan Sulphate ◽  
Carbonyl Oxygen ◽  
Dimethyl Sulphoxide ◽  
Coupling Constants

The 1H-n.m.r. spectra of solutions in [2H6]dimethyl sulphoxide of the sodium salts of tetra-, hexa- and octa-saccharides prepared from hyaluronate by testicular-hyaluronidase digestion were examined at 300 and 500 MHz. The signals from hydroxy groups at positions 2 and 3 in the glucuronic acid moiety were assigned. Their chemical shifts and associated temperature-dependencies, as well as their coupling constants, depended on whether or not the uronic acid was at the non-reducing end. Deviations from the ‘normal’ pattern of hydroxy-group proton n.m.r. behaviour were attributable to participation in hydrogen bonds, either to the acetamido carbonyl oxygen atom or the pyranose ring oxygen atom of neighbouring N-acetylhexosamine moieties. A secondary structure, containing four different hydrogen bonds per trisaccharide unit of glucuronsyl-hexosaminyl-glucuronic acid, was demonstrated. This is the first complete and detailed secondary structure to be established for hyaluronate in any solvent. Hyaluronate is compared with chondroitin sulphate, dermatan sulphate, heparan sulphate and keratan sulphate in their potential to form secondary structures with features in common. The significance of the details of the structure to its overall stability, and the probability of their persistence into aqueous environments, are discussed. The presence of all or most of the secondary structure in glycosaminoglycuronans is correlated with a space-filling function in the tissue, and with a high carbohydrate content in the parent proteoglycan in the case of the chondroitin sulphates.

REACTIONS OF AMIDES AND RELATED COMPOUNDS: I. N.M.R. (PROTON) INVESTIGATION OF N,N-DIMETHYLFORMAMIDE – LEWIS ACID ADDUCTS AND REMARKS ON THE RELATIVE STRENGTH OF LEWIS ACIDS

1965 ◽  
Vol 43 (2) ◽  
pp. 375-380 ◽  
Author(s):  
Stephen J. Kuhn ◽  
John S. McIntyre
Keyword(s):  
Chemical Shift ◽  
Lewis Acid ◽  
Lewis Acids ◽  
Methylene Chloride ◽  
Carbonyl Oxygen ◽  
Relative Strength ◽  
Proton Resonance ◽  
Lewis Acid Adducts ◽  
Related Compounds ◽  
Good Agreement

The proton resonance spectra of a number of Lewis acid – N,N-dimethylformamide adducts in 2-nitropropane and methylene chloride solutions have been investigated and an attempt has been made to correlate the relative strength of Lewis acids with the chemical shift of the methyl protons. The order obtained for the relative strength of Lewis acids shows good agreement with the results obtained by other methods. The complex formation has taken place on the carbonyl oxygen of the N,N-dimethylformamide in all cases. The DMF – Lewis acid mole ratios were 1:1 in ZnCl2, AlCl3, PF5, BiCl3, InCl3, AsF5, SbCl5, SbF5, BF3, BCl3, BBr3. The 2:1 DMF – Lewis acid complexes of ZnCl2, SnCl4, SnBr4, Snl4, TiCl4, ZrBr4 have also been investigated.

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