Nuclear Overhauser Effect Spectroscopy Spectra Research Articles

Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations.

The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol–1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII′-bend-like motif at the Gly3–Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII′ bend at the Gly2–Gly3 sequence and a βI bend at the Gly3–Phe4 sequence. The calculated ensemble-averaged distance between CGly2α and CLeu5α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the “bioactive conformation” like an extended structure when binding to δOR.

Use of Diethanolamine as a Viscous Solvent for Mixture Analysis by Multidimensional Heteronuclear ViscY NMR Experiments.

Diethanolamine/DMSO-d6 as a viscous binary solvent is first reported for the individualization of low-polarity mixture components by multidimensional heteronuclear ViscY NMR experiments under spin diffusion conditions. Solvent viscosity induces the slowing down of molecular tumbling, hence promoting magnetization transfer by dipolar longitudinal cross-relaxation. As a result, all 1H nuclei resonances within the same molecule may correlate in a 2D nuclear Overhauser effect spectroscopy (NOESY) spectrum, giving access to mixture analysis. We offer a new way to analyze mixtures by considering 3D heteronuclear heteronuclear single-quantum coherence-NOESY (HSQC-NOESY) experiments under viscous conditions. We state the individualization of four low-polarity chemical compounds dissolved in the diethanolamine/DMSO-d6 solvent blend using homonuclear selective 1D, 2D 1H-1H NOESY experiments and heteronuclear 1D, 2D 1H-19F heteronuclear Overhauser effect spectroscopy, 2D 1H-19F, 1H-31P HSQC-NOESY, and 3D 1H-19F-1H, 1H-31P-1H HSQC-NOESY experiments by taking profit from spin diffusion.

Carrier-Free Deferoxamine Nanoparticles against Iron Overload in Brain

Carrier-Free Deferoxamine Nanoparticles against Iron Overload in Brain

Determination of tautomeric preference of fenobam in solution by high-resolution NMR spectroscopy.

In this work, tautomeric preference of fenobam in solution was investigated by homonuclear and heteronuclear solution nuclear magnetic resonance (NMR) spectroscopy. 1 H-1 H nuclear Overhauser effect spectroscopy (NOESY) spectrum revealed that fenobam in liquid state exists exclusively in one of the two possible tautomeric structures, which was confirmed by 1 H-13 C HSQC and heteronuclear multiple bond correlation (HMBC) spectra. Moreover, difference between the two tautomeric structures was studied by theoretical calculations, which further proved the result obtained by the NMR experiments.

Comparison of Regular, Pure Shift, and Fast 2D NMR Experiments for Determination of the Geographical Origin of Walnuts

1H NMR spectroscopy, in combination with chemometric methods, was used to analyze the methanol/acetonitrile (1:1) extract of walnut (Juglans Regia L.) regarding the geographical origin of 128 authentic samples from different countries (France, Germany, China) and harvest years (2016–2019). Due to the large number of different metabolites within the acetonitrile/methanol extract, the one-dimensional (1D) 1H NOESY (nuclear Overhauser effect spectroscopy) spectra suffer from strongly overlapping signals. The identification of specific metabolites and statistical analysis are complicated. The use of pure shift 1H NMR spectra such as PSYCHE (pure shift yielded by chirp excitation) or two-dimensional ASAP-HSQC (acceleration by sharing adjacent polarization-heteronuclear single quantum correlation) spectra for multivariate analysis to determine the geographical origin of foods may be a promising method. Different types of NMR spectra (1D 1H NOESY, PSYCHE, and ASAP-HSQC) were acquired for each of the 128 walnut samples and the results of the statistical analysis were compared. A support vector machine classifier was applied for differentiation of samples from Germany/China, France/Germany, and France/China. The models obtained by conduction of a repeated nested cross-validation showed accuracies from 58.9% (±1.3%) to 95.9% (±0.8%). The potential of the 1H-13C HSQC as a 2D NMR experiment for metabolomics studies was shown.

Adaptive Chirality of an Achiral Cage: Chirality Transfer, Induction, and Circularly Polarized Luminescence through Aqueous Host–Guest Complexation

Chirality transfer, induction, and circularly polarized luminescence (CPL) using supramolecular hosts, such as macrocycles and cages, have been explored for wide-ranging applications in chiral reco...

HR-1 H NMR spectroscopy and multivariate statistical analysis to determine the composition of herbal mixtures for infusions.

The ever-growing diffusion and consumption of herbal teas, due to their sensory attributes and well-known health benefits exposes them to the real risk of adulteration, especially in the case of commercial mixtures already minced for infusion. Therefore, novel and suitable tools for the control of these valuable products are increasingly required. This work provides new insights for the authenticity study of infusions. The main objective was verifying the potential of proton nuclear magnetic resonance (1 H-NMR) combined with partial least square (PLS) regression to build highly predictive models, useful for the determination of the real amounts of herbs in mixtures, by the simple analysis of the related infusion. Peppermint, fennel, lemon balm, and passiflora were chosen to set-up an experimental plan according to a central composite design (CCD). One-dimensional nuclear Overhauser effect spectroscopy (1D-NOESY) spectra were properly pretreated and then analysed by chemometrics to extract significant information from the raw data. Venetian-blind cross-validation and different chemometric indicators (RMSEC, RMSECV, RMSEP, R2 CAL , R2 CV, R2 PRED ) were used to establish the best model, which include four factors explaining 88.70 and 83.77% of the total variance in X and Y, respectively. These promising results have laid the basis for further development of the method, to extend its applicability and make it more scalable. This tool could replace expensive separative techniques and protect the rights of consumers with particular attention to safety issues and quality assurance.

Molecular conformational evolution mechanism during nucleation of crystals in solution.

Nucleation of crystals from solution is fundamental to many natural and industrial processes. In this work, the molecular mechanism of conformational polymorphism nucleation and the links between the molecular conformation in solutions and in crystals were investigated in detail by using 5-nitro-furazone as the model compound. Different polymorphs were prepared, and the conformations in solutions obtained by dissolving different polymorphs were analysed and compared. The solutions of 5-nitro-furazone were proven to contain multiple conformers through quantum chemical computation, Raman spectra analysis, 2D nuclear Overhauser effect spectroscopy spectra analysis and molecular dynamics simulation. The conformational evolution and desolvation path was illustrated according to the 1H NMR spectra of solutions with different concentrations. Finally, based on all the above analysis, the molecular conformational evolution path during nucleation of 5-nitro-furazone was illustrated. The results presented in this work shed a new light on the molecular mechanism of conformational polymorphism nucleation in solution.

Three New Sesquiterpenoids from the Algal-Derived Fungus Penicillium chermesinum EN-480.

Secondary metabolites obtained from marine-derived fungi are rich sources of drug candidates. Three new sesquiterpenoids, chermesiterpenoids A–C (1–3), along with four known alkaloids (4–7), were isolated and identified from the marine red algal-derived fungus Penicillium chermesinum EN-480. The structures of these new sesquiterpenoids were elucidated using detailed analysis of the NMR data and their relative configurations were elucidated using nuclear overhauser effect spectroscopy (NOESY) spectra as well as gauge-independent atomic orbital (GIAO) NMR shift calculations and DP4+ probability analysis. Their absolute configurations were determined using electronic circular dichroism (ECD) calculations and modified Mosher’s method. Compounds 2 and 3 exhibited potent activities against human and aquatic pathogenic bacteria and plant pathogenic fungi.

Specificity of Counterion Binding to a Conjugated Polyelectrolyte: A Combined Molecular Dynamics and NOESY Investigation.

Poly(thiophen-3-ylacetic acid) (PTAA) is a representative of conjugated polyelectrolytes which are used in many optoelectronics devices. The performance of these devices is affected by the polymer conformation, which, among others, depends on the nature of the counterion. In this study, the binding of tetrabutylammonium counterions (TBA+) on PTAA was determined using a combination of nuclear Overhauser effect spectroscopy (NOESY) and molecular dynamics (MD) simulation. It was found that TBA+ ions specifically bind on the hydrophobic main chain of PTAA, while, according to MD simulations, alkali counterions predominantly bind in the vicinity of negatively charged carboxylic groups located on side chains. The MD trajectories were used to compute the relaxation matrices and the NOESY spectra. With the help of these latter calculations, the changes of intensities in experimental NOESY spectra upon binding of TBA+ ions to PTAA were interpreted.

Preparation and physicochemical characterization of inclusion complexes derived from phytosterols and β-cyclodextrin

Phytosterols (PS), that is vegetable sterols, are compounds widely recognized for lowering the absorption of cholesterol and decreasing cancer risk, with &amp;#946;sitosterol, stigmasterol and campesterol being the most abundant. As PS is poorly soluble in aqueous solutions, many approaches have been proposed to increase their solubility and bioavailability. &amp;#946;-cyclodextrin (&amp;#946;-CD) could be used to increase PS aqueous solubility because of its capacity to entrap a variety of hydrophobic guest molecules in its cavity. In this work, the formation of &amp;#946;-CD/PS inclusion complexes was confirmed by Differential Scanning Calorimetry (DSC), Electrospray Ionization-High Resolution Mass Spectrometry (ESIHRMS) and Fourier Transform Infrared Spectroscopy (FT-IR), while structural characteristics were determined by one- and two-dimensional Nuclear Magnetic Resonance (NMR) techniques. Results confirmed 1:1 binding stoichiometry, which suggests the total inclusion of rings and chains of the different PS. The hypothesis of folding of the lateral chains into the cavity may be supported by the multiple correlations observed in the Nuclear Overhauser Effect Spectroscopy (NOESY) and rotatingframe Nuclear Overhauser Effect Spectroscopy (ROESY) spectra.

Dimethyl 2,2'-[2,2'-(ethane-1,1-diyl)bis(1H-indole-3,2-diyl)]-diacetate: a small molecule capable of nano-scale assembly, inhibiting venous thrombosis and inducing no bleeding side effect.

BackgroundDue to the discovery that deep venous thrombosis (DVT) inhibitor is of chemotherapeutic importance, the nano-property of dimethyl 2,2′-[2,2′-(ethane-1,1-diyl) bis(1H-indole-3,2-diyl)]-diacetate (DEBIC), a recently reported antitumor agent, is worthy of characterization.Materials and methodsOne-pot reaction was used to prepare DEBIC. Electrospray Ionization (+/−)-Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometer (ESI(+/−)-FT-ICR-MS), quadrupole Collision Induced Dissociation (qCID) and nuclear overhauser effect spectroscopy spectra were used to present the assembly of DEBIC. Transmission electron microscopy, scanning electron microscopy, atomic force microscopy and Faraday–Tyndall effect were used to visualize the nano-property of DEBIC. Rat models were used to evaluate DVT inhibition and the bleeding reaction of DEBIC.ResultsOne-pot reaction can provide DEBIC in acceptable yield and high purity. In water, rat plasma and lyophilized powders of DEBIC existed as particles of small nano-size. In vivo DEBIC inhibited DVT in a dose-dependent manner. The minimal effective dose of DEBIC was 1.7 μmol/kg. Even the dose of 36 μmol/kg/day DEBIC did not induce bleeding side effect in DVT rats like in warfarin (0.82 μmol/kg/day).ConclusionDEBIC is a small molecule capable of nano-scale assembly, inhibiting venous thrombosis and inducing no bleeding side effect.

Four New C9 Metabolites from the Sponge-Associated Fungus Gliomastix sp. ZSDS1-F7-2

Four new structurally related metabolites, one γ-lactone named gliomasolide F (1), one δ-lactone named gliomasolide G (2), and two medium-chain fatty acids named gliomacids A–B (3–4), each containing nine carbons in total, were identified from the sponge-associated fungus Gliomastix sp. ZSDS1-F7-2. The planar chemical structures of these novel C9 metabolites were elucidated by nuclear magnetic resonance (NMR) spectroscopic methods, in connection with the analysis of high-resolution mass spectrometry (HRMS) and infrared (IR) data. The absolute configuration of 1, was determined by comparisons of experimental circular dichroism (CD) and optical rotation (OR) value with corresponding ones computed by quantum chemistry. The relative configuration of 2 was determined by the Nuclear Overhauser effect spectroscopy (NOESY) spectrum, while its absolute configuration was tentatively determined in view of the biogenetic and biosynthetic relationships between 1 and 2. Compounds 3–4, originally as an inseparable mixture, were successfully isolated after chemical modifications. The stereo-chemistries of compounds 3–4 were assumed by comparison of 13C NMR with those of the similar moiety reported in literature, in addition to the biogenetic and biosynthetic relationships with 1. The plausible biosynthetic relationships among these four C9 metabolites were supposed. Biologically, compounds 1–4 showed no cytotoxic effect against HeLa cell line at concentrations up to 25 μg/mL, while 1 exhibited moderate antifouling activity against the settlement of Balanus amphitrite larvae with IC50 being 12.8 μg/mL and LC50 > 25 μg/mL. The co-occurrence of macrolides gliomasolides A—E and four C9 metabolites in the same fermentation culture made us assume that these C9 metabolites might be biosynthetic building blocks toward the construction of more complex macrolides such as gliomasolides A—E or other unidentified polyketides.

Rotation of Guanine Amino Groups in G-Quadruplexes: A Probe for Local Structure and Ligand Binding

Nucleic acids are dynamic molecules whose functions may depend on their conformational fluctuations and local motions. In particular, amino groups are dynamic components of nucleic acids that participate in the formation of various secondary structures such as G-quadruplexes. Here, we present a cost-efficient NMR method to quantify the rotational dynamics of guanine amino groups in G-quadruplex nucleic acids. An isolated spectrum of amino protons from a specific tetrad-bound guanine can be extracted from the nuclear Overhauser effect spectroscopy spectrum based on the close proximity between the intra-residue imino and amino protons. We apply the method in different structural contexts of G-quadruplexes and their complexes. Our results highlight the role of stacking and hydrogen-bond interactions in restraining amino-group rotation. The measurement of the rotation rate of individual amino groups could give insight into the dynamic processes occurring at specific locations within G-quadruplex nucleic acids, providing valuable probes for local structure, dynamics, and ligand binding.

Identification and Characterization of 3-epi-Rotundone, a Novel Stereoisomer of Rotundone, in Several Kinds of Fruits.

A novel stereoisomer of rotundone, 3-epi-rotundone, was identified in the aroma of grapefruit, orange, apple, and mango. 3-epi-Rotundone was prepared by the isomerization of rotundone, and its structural elucidation was confirmed by comparing the 1D and 2D nuclear magnetic resonance and nuclear Overhauser effect spectroscopy spectra with those of rotundone. The odor thresholds of rotundone and 3-epi-rotundone in water were determined by a triangle test as 5 and 19100 ng/kg, respectively. The odor of 3-epi-rotundone was evaluated as woody, spicy, peppery, citrus, grapefruit-like, powdery, and celery-like, which was a greater range of odor characteristics than that for rotundone. Results of odor evaluation of 3-epi-rotundone revealed that its unique organoleptic properties, which were odor description (woody, spicy, and peppery), anosmic properties in neat form, and strong adaptation, were similar to those of rotundone. 3-epi-Rotundone might be a valuable substance to apply new types of woody, peppery, and spicy notes.

Strategic synthesis and in vitro antimicrobial evaluation of novel difluoromethylated 1-(1, 3-diphenyl-1H-pyrazol-4-yl)-3, 3-difluoro-1, 3-dihydro-indol-2-ones

A strategic synthesis of 1-(1,3-diphenyl-1H-pyrazol-4-yl)-3,3-difluoro-1,3-dihydro-indol-2-ones has been achieved by the reaction of indole-2,3-dione (isatin) and substituted bromoacetyl benzene followed by cyclization reaction and evaluated for in vitro antibacterial and antifungal activities. Direct fluorination using diethylaminosulfur trifluoride as a nucleophilic fluorinating reagent was carried out in the present paper. Undoubtedly this methodology gives a facile and straightforward pathway to construct 1-(1,3-diphenyl-1H-pyrazol-4-yl)-3,3-difluoro-1,3-dihydro-indol-2-ones in good yields. The structure of new fluorinated 1-(1,3-diphenyl-1H-pyrazol-4-yl)-3,3-difluoro-1,3-dihydro-indol-2-ones was characterized based on 1H, 13C, and 19F nuclear magnetic resonance spectroscopy and mass spectrometry data. Structure of target compound was confirmed by Nuclear Overhauser Effect Spectroscopy spectra. Some of the synthesized compounds showed good antimicrobial activities against bacteria and fungi.

Casein Phosphopeptide-Amorphous Calcium Phosphate Nanocomplexes: A Structural Model.

Tryptic digestion of the calcium-sensitive caseins yields casein phosphopeptides (CPP) that contain clusters of phosphorylated seryl residues. The CPP stabilize calcium and phosphate ions through the formation of complexes. The calcium phosphate in these complexes is biologically available for intestinal absorption and remineralization of subsurface lesions in tooth enamel. We have studied the structure of the complexes formed by the CPP with calcium phosphate using a variety of nuclear magnetic resonance (NMR) techniques. Translational diffusion measurements indicated that the β-CN(1-25)-ACP nanocomplex has a hydrodynamic radius of 1.526 ± 0.044 nm at pH 6.0, which increases to 1.923 ± 0.082 nm at pH 9.0. (1)H NMR spectra were well resolved, and (3)JH(N)-H(α) measurements ranged from a low of 5.5 Hz to a high of 8.1 Hz. Total correlation spectroscopy and nuclear Overhauser effect spectroscopy spectra were acquired and sequentially assigned. Experiments described in this paper have allowed the development of a structural model of the β-CN(1-25)-amorphous calcium phosphate nanocomplex.

Antiproliferative and antioxidative effects of novel hydrazone derivatives bearing coumarin and chromene moiety

Open image in new window A series of new hybrid molecules with a hydrazone fragment were synthesized and characterized by Fourier transform-infrared spectroscopy, nuclear magnetic resonance, mass spectrometry, and elemental analysis. The nuclear magnetic resonance spectra of the hydrazones 4a–c showed exchange of syn and antiperiplanar conformers around the amide bond, the more stable being the antiperiplanar one. The nuclear Overhauser effect spectroscopy (NOESY) spectra confirm E configuration around C=N bond. The tested compounds exhibited concentration-dependent cytotoxic effects against human tumor cell lines in a micromolar range (MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) tetrazolium reduction assay). Hydrazone 4a proved to be the most potent antiproliferative agent of the series. Within the antioxidant screening 8b exhibited the highest radical scavenging activity (% RSA max) and the largest rate constant for the reaction with 2,2-diphenyl-1-picrylhydrazyl.

Highly Viscous Binary Solvents: DMSO-d6/Glycerol and DMSO-d6/Glycerol-d8 for Polar and Apolar Mixture Analysis by NMR.

The use of two new highly viscous binary solvents, DMSO-d6/glycerol (GL) and DMSO-d6/glycerol-d8 (GL-d8), is reported for the first time in order to give access to the individual NMR spectra of mixture components. Their high dissolution power offers a wide range of potential applications to mixture analysis, regardless of polarity. Under particular conditions of viscosity, the tumbling rate of small and medium-sized molecules slows down in solution, so that the longitudinal cross-relaxation regime favors the observation of spin diffusion. As a consequence, all the resonances of the (1)H nuclei within the same molecule tend to correlate together in a 2D nuclear Overhauser effect spectroscopy (NOESY) spectrum, thus opening the way to mixture analysis. This work reports the analysis of a polar mixture composed of Leu-Val, Leu-Tyr, Gly-Tyr, and Ala-Tyr dissolved in DMSO-d6/GL (8:2, v/v) and of an apolar mixture made of β-ionone, (±)-citronellal, (+)-limonene, and flavone dissolved in DMSO-d6/GL-d8 (5:5, v/v) by means of spin diffusion in homonuclear selective 1D NOESY, selective 2D NOESY, NOESY-correlation spectroscopy (COSY), NOESY-total correlation spectroscopy (TOCSY) experiments, and 2D heteronuclear single-quantum correlation spectroscopy (HSQC)-NOESY. DMSO-d6/GL must be preferred to DMSO-d6/GL-d8 for the study of biological active compounds in which labile protons must not be exchanged by deuterium nuclei. DMSO-d6/GL-d8 is more appropriate for organic compounds in which labile protons are not essential to the structure elucidation. DMSO-d6/GL and DMSO-d6/GL-d8 binary mixture solvents seem to be so far the most efficient viscous solvents described in the literature for the resolution of both polar and apolar complex mixtures components by NMR spin diffusion.

Nuclear overhauser spectroscopy of chiral CHD methylene groups.

Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure.