NMR Spectral Properties Research Articles

Synthesis, Photophysical, Solvatochromic and DFT Studies of Newer 1-(2-(naphthalen-2-yl)-2-oxoethyl) pyridin-1-ium bromide

A newer pyridinium compound was synthesized under microwave irradiation by reaction of pyridine and 2-bromo-1-(naphthalen-2-yl)ethanone. The pyridinium compound was characterized by mass, IR, 1H NMR, 13C NMR spectral analysis, also photophysical, solvatochromic, and thermal properties of newer pyridinium compound were investigated. Solvent dependent optical properties of pyridinium compound with range of solvents with varying polaritieswere studied using Lippert-Mataga plot and solvent polarity empirical parameter ET(30). The thermal stability and phase behavior were studied by TGA and DSC analysis at a heating rate of 10 deg min-1. DFT computation was performed to get the optimized molecular orbitals and HOMO - LUMO energies.

Termination of the Chirality Confusion of Peribysins

Abstract Peribysins belong to a family of eremophilanes isolated from marine Periconia byssoides OUPS-N133 and terrestrial P. macrospinosa KT3863. Their absolute configurations were determined to be the (4S)-enantiomers based on the modified Mosher’s method, chemical derivatizations, density functional theory (DFT)-based electronic circular dichroism (ECD) spectral analysis, and DFT-based [α]D calculations. Danishefsky’s and Reddy’s total syntheses assigned the (4R)-forms for the marine peribysins despite agreeing with the (4S)-configuration for the terrestrial peribysin Q (5). This paper reports the successful solution of this chirality confusion of peribysins by reproducing the ECD spectrum of peribysin G bis(p-bromobenzoate) prepared from peribysin A (1) isolated from terrestrial P. byssoides TS60. 2β-Hydroxyperibysin A (6), which was isolated by changing the culture conditions of the above fungus, was converted to (4S)-peribysin E MTPA esters. These compounds showed identical 1H NMR spectral properties to those reported in the isolation paper.

Occurrence of a resveratrol trimer diglucoside derivative with a fused heptacyclic skeleton in Shorea uliginosa

Uliginoside H ( 1 ) is a new resveratrol trimer diglucoside derivative with fused heptacycles. It was discovered from the acetone extract of the stem bark of Shorea uliginosa (Dipterocarpaceae). Spectroscopic analysis, such as NMR experiments, was used to elucidate the structure, and the absolute configuration was determined using circular dichroism data. Notably, 1 has a fused ring system composed of a dihydrobenzofuran ring, a hexahydrocyclopenta[ c ]chromene ring, and a cyclohex-2-enone ring, each with eight asymmetric carbons. Thus, a plausible biosynthetic pathway for 1 was proposed. • Uliginoside H is a C -di-glucoside of trimeric resveratrol. • Uliginoside H is isolated from Shorea uliginosa . • Absolute configuration was determined based on NMR and CD spectral properties. • Structure of the core heterocyclic skeleton bearing dearomatized ring was elucidated. • The plausible biosynthetic pathway was proposed.

Nano SiO2 catalytic synthesis, NMR spectral studies, photophysical properties and theoretical studies of some styryl imidazole derivatives

New styryl imidazole derivatives were prepared by using nano SiO2 catalyst and proved it catalytic efficiency. Diminutive reaction time, high yield of the imidazole derivatives and a variety of substitute reactant usage were accomplished by using nano SiO2 catalyst. Solvatochromism of newly synthesized imidazole derivatives have been studied by using Marcus and Reichardt – Dimroth solvent functions. When polarity of the solvent was increased, the absorption position of synthesized styryl imidazole derivatives shifted to higher wavelength, that is bathochromic shift was fashioned. Emission band maxima these imidazole derivatives also shifted to the longer wavelength, which was due to dielectric solute and solvent interactions. HOMO–LUMO energies of imidazole derivatives have been calculated by DFT calculations at B3LYP/6-31G (d, p) using Gaussian-03.

Protonation of the oxo-bridged heme/copper assemblies: Modeling the oxidized state of the cytochrome c oxidase active site

In this study on model compounds for the resting oxidized state of the iron‑copper binuclear center in cytochrome c oxidase (CcO), we describe the synthesis of a new μ-oxo-heme/Cu complex, [(TPP)FeIII–O–CuII(tmpa)][B(C6F5)4] (2) {TPP: tetraphenyl porphyrinate(2–); TMPA: tris(2-pyridylmethylamine)}, as well as two protonation events for three μ-oxo-heme/Cu complexes with varying peripheral substituents on the heme site. The addition of increasing amounts of strong acid to these μ-oxo-heme/Cu systems successively led to the generation of the corresponding μ-hydroxo, μ-aquo, and the dissociated complexes. The heme/Cu assemblies bridged through a water ligand are reported here for the first time and the 1H NMR and 19F NMR spectral properties are consistent with antiferromagnetically coupled high-spin iron(III) and copper(II) centers. By titration using a series of protonated amines, the pKa values for the corresponding μ-hydroxo-heme/Cu species (i.e., the first protonation event) have been reported and compared with the pKa ranges previously estimated for related systems. These synthetic systems may represent structural models for the oxidized FeIII–X–CuII resting state, or turnover intermediates and can be employed to clarify the nature of proton/electron transfer events in CcO. SynopsisThe resting oxidized state of the cytochrome c oxidase active site contains an Fea3−OHx−CuB moiety. Here, we investigated two successive protonation events, for a series of μ-oxo-heme/Cu assemblies and reported the pKa values for the first protonation event. The μ-aquo-heme/Cu complexes described here are the first examples of such systems.

Do polyproline II helix associations modulate biomolecular condensates?

Biomolecular condensates are microdroplets that form inside cells and serve to selectively concentrate proteins, RNAs and other molecules for a variety of physiological functions, but can contribute to cancer, neurodegenerative diseases and viral infections. The formation of these condensates is driven by weak, transient interactions between molecules. These weak associations can operate at the level of whole protein domains, elements of secondary structure or even moieties composed of just a few atoms. Different types of condensates do not generally combine to form larger microdroplets, suggesting that each uses a distinct class of attractive interactions. Here, we address whether polyproline II (PPII) helices mediate condensate formation. By combining with PPII‐binding elements such as GYF, WW, profilin, SH3 or OCRE domains, PPII helices help form lipid rafts, nuclear speckles, P‐body‐like neuronal granules, enhancer complexes and other condensates. The number of PPII helical tracts or tandem PPII‐binding domains can strongly influence condensate stability. Many PPII helices have a low content of proline residues, which hinders their identification. Recently, we characterized the NMR spectral properties of a Gly‐rich, Pro‐poor protein composed of six PPII helices. Based on those results, we predicted that many Gly‐rich segments may form PPII helices and interact with PPII‐binding domains. This prediction is being tested and could join the palette of verified interactions contributing to biomolecular condensate formation.

Stereospecific Synthesis of Cyclic Sulfite Esters with Sulfur-Centered Chirality via Diastereoselective Strategy and Intramolecular H-Bonding Assistance.

Stereospecific synthesis of several cyclic sulfite esters containing three stereogenic centers from enantiopure 1,1,4,4-tetraarylbutanetetraols was achieved. Chiral sulfur centers were constructed stereospecifically via a diastereoselective reaction with the assistance of an intramolecular H-bonding interaction. The absolute configuration of the S atom was elucidated by using the corresponding single-crystal X-ray diffraction analysis of the synthesized monochloride cyclic sulfite esters. Furthermore, a crystallographic evidence of the specific intramolecular C(sp3)-H···CAr weak H-bondings was presented, and its dramatic effect on the 1H NMR spectral properties was revealed. This intriguing behavior was unambiguously rationalized by different shielding effects of the neighboring phenyl rings. Additionally, the theoretical results obtained on the basis of MP2 calculations fully supported the existence of intramolecular hydrogen bonding interactions being responsible for the observed unique chemical and spectral properties.

Rapid prediction of NMR spectral properties with quantified uncertainty

Accurate calculation of specific spectral properties for NMR is an important step for molecular structure elucidation. Here we report the development of a novel machine learning technique for accurately predicting chemical shifts of both {^1mathrm{H}} and {^{13}mathrm{C}} nuclei which exceeds DFT-accessible accuracy for {^{13}mathrm{C}} and {^1mathrm{H}} for a subset of nuclei, while being orders of magnitude more performant. Our method produces estimates of uncertainty, allowing for robust and confident predictions, and suggests future avenues for improved performance.

Partial substitution of chemical fertilizer with organic amendments affects soil organic carbon composition and stability in a greenhouse vegetable production system

Understanding soil organic carbon (SOC) composition and stability is necessary for long-term carbon (C) sequestration. Fertilization is known to modify SOC stability and composition; however, inconsistent results have been reported. Here, we evaluated the changes in SOC composition and stability through multiple methods in an 8-year fertilization experiment under greenhouse vegetable production (GVP) systems in Tianjin, China. This experiment was designed to supply an equivalent amount of nutrients (N, P2O5 and K2O) but variable amount of C through different exogenous organic resources (ORs) input. Five treatments were included based on substitution of chemical fertilizer nitrogen (N) with different exogenous ORs: no N (no nitrogen inputs), 4/4CN (CN, nitrogen in chemical fertilizer), 2/4CN + 2/4 MN (MN, nitrogen in pig manure, high-quality ORs), 2/4CN + 2/4SN (SN, nitrogen in corn straw, low-quality ORs) and 2/4CN + 1/4 MN+1/4SN. Organic fertilization strategies promoted SOC accumulation and reduced SOC stability by increasing labile C fractions, whereas chemical fertilizer alone had a negative effect on SOC accumulation by consuming labile C fractions but enhanced SOC stability. Notably, the characteristics of high temperature, nutrient availability and C inputs in organically managed soils in GVP systems weaken the influence of ORs quality on SOC stability. Consequently, high doses of C inputs (11.5 and 18.5 Mg ha–1 year–1 in 2/4CN + 1/4 MN+1/4SN and 2/4CN + 2/4SN treatments) induced lower SOC stability than low doses of C inputs (4.5 Mg ha–1 year–1 in the 2/4CN + 2/4 MN treatment), irrespective of ORs quality. In addition, strong correlations were found between SOC thermal characteristics and SOC chemical and 13C NMR spectral properties, indicating that thermal analysis techniques can characterize SOC stability effectively.

Identification of Unknown Metabolomics Mixture Compounds by Combining NMR, MS, and Cheminformatics.

Metabolomics aims at the comprehensive identification of metabolites in complex mixtures to characterize the state of a biological system and elucidate their roles in biochemical pathways. For many biological samples, a large number of spectral features observed by NMR spectroscopy and mass spectrometry (MS) belong to unknowns, i.e., these features do not belong to metabolites that have been previously identified, and their spectral information is not available in databases. By combining NMR, MS, and combinatorial cheminformatics, the analysis of unknowns can be pursued in complex mixtures requiring minimal purification. This chapter describes the SUMMIT MS/NMR approach covering sample preparation, NMR and MS data collection and processing, and the identification of likely unknowns with the use of cheminformatics tools and the prediction of NMR spectral properties.

Automated projection spectroscopy in solid-state NMR.

Given that solid-state NMR is being used for protein samples of increasing molecular weight and complexity, higher-dimensionality methods are likely to be more and more indispensable for unambiguous chemical shift assignments in the near future. In addition, solid-state NMR spectral properties are increasingly comparable with solution NMR, allowing adaptation of more sophisticated solution NMR strategies for the solid state in addition to the conventional methodology. Assessing first principles, here we demonstrate the application of automated projection spectroscopy for a micro-crystalline protein in the solid state.

Study on absorption and spectral properties of H2S in carboxylate protic ionic liquids with low viscosity

The exorbitant price and high viscosity are two major disadvantages for ionic liquids (ILs), which influence their practical applications in gas separation. Here we synthesized ten carboxylate protic ionic liquids (PILs), containing N-ethylmorpholine acetate, N-ethylmorpholine propionate, N-ethylmorpholine butyrate, N-ethylmorpholine methoxylacetate, 4-(2-hydroxyethyl) morpholine acetate, and 4-(2-hydroxyethyl) morpholine methoxyacetate, triethylamine acetate, triethylamine propionate, triethylamine propionate, and triethylamine methoxylacetate, with low cost and viscosity for absorption of H2S. The densities and viscosities of these carboxylate PILs were measured in the temperature range of (298.2 to 333.2) K at atmospheric pressure. The solubility of H2S in these PILs was determined using an isochoric saturation technique at 298.2–318.2 K and 0–1.096 bar. It was found that the solubility of H2S in these PILs increased with the increasing pressure and length of the alkyl chains on the carboxylic acid. The absorption processes obeyed Henry's law within the given experimental conditions and Henry's constants were calculated from solubility data. In addition, the FTIR and NMR spectral properties in the absorption process of H2S in N-ethylmorpholine butyrate [NEMH][Bu] also were investigated to present important information on absorption mechanism. The results indicated that [NEMH][Bu] demonstrated a highest absorption capacity among these PILs and absorption of H2S is a physical behavior. Comparisons of PILs with the common ILs and organic solvents were also done to demonstrate the advantages of PILs.

FT-IR, UV–visible, and NMR Spectral Analyses, Molecular Structure, and Properties of Nevadensin Revealed by Density Functional Theory and Molecular Docking

ABSTRACTNevadensin 2-(4-methoxyphenyl)-5,7-dihydroxy-6,8-dimethoxy-4H-1-benzo-pyran-4-one] is a natural bioactive flavonoid compound that has the potential to become a novel “natural lead” in the field of drug discovery program. The molecular structure, vibrational frequencies, and corresponding vibrational assignment of nevadensin have been investigated experimentally and theoretically by employing the B3PW91/6–311++G(d,p) method. The fundamental vibrational wave numbers as well as their intensities were calculated, and a good correlation between experimental and scaled calculated wave numbers had been accomplished. The ultraviolet spectrum of the studied molecule was recorded in the region 200–500 nm, and the electronic properties were predicted by the time-dependent density functional theory approach. 1H and 13C NMR spectra have been calculated by employing the gauge-independent atomic orbital method. Nevadensin has been reported to exhibit antimicrobial activities against both Gram-positive and Gram-negative bacteria and also against the fungal pathogens, highlighting the pharmacological importance of the molecule.

Cooperative Effect of Spacer and Lewis Base on Highly Reversible Spectral Changes of the Octaethylporphyrin Chromatic System in Sensitivity, Stability, and Visibility to Trifluoroacetic Acid

Abstract The diacetylene-group connected chromatic system of [octaethylporphyrin]-[spacer]-[Lewis base] triads (OEP-SPC-LB) was conclusively studied, in which a trigger-like interaction of the terminal LB with trifluoroacetic acid (TFA) dramatically affects the inherent electronic properties of OEP. The 1H NMR, IR, and electronic absorption spectral properties of these OEP derivatives were examined, and were contemplated in view of a cooperative effect of SPC and LB on their OEP nucleus. Based on the results from this study, the structural elements for molecular design will be proposed in order to improve their reversible spectral changes between neutral and acidic media in terms of sensitivity, stability, and visibility to TFA.

Synthesis and anticancer activity evaluation of (E)-3-{[5-(aryl)-1,3,4-oxadiazol-2-yl]methyl}-5-(3,4,5-trimethoxybenzylidene)thiazolidine-2,4-diones

A series of new substituted (E)-3-{[5-(aryl)-1,3,4-oxadiazol-2-yl]methyl}-5-(3,4,5-trimethoxy-benzylidene) thiazolidine-2,4-diones have been synthesized. The products have been characterized by their IR, 1H NMR, 13C NMR, and mass spectral properties and evaluated for anticancer activity against four human cancer cell lines: A549, A375, MCF-7, and HT-29.

Six, Seven or Eight Coordinate Fe(II) , Co(II) or Ni(II) Complexes of Amide-Appended Tetraazamacrocycles for ParaCEST Thermometry.

Fe(II) , Co(II) and Ni(II) complexes of two tetraazamacrocycles (1,4,8,11-tetrakis(carbamoylmethyl)-1,4,8,11-tetraazacyclotetradecane (L1) and 1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane (L2) show promise as paraCEST agents for registration of temperature (paraCEST=paramagnetic chemical exchange saturation transfer). The Fe(II) , Co(II) and Ni(II) complexes of L1 show up to four CEST peaks shifted ≤112 ppm, whereas analogous complexes of L2 show only a single CEST peak at ≤69 ppm. Comparison of the temperature coefficients (CT ) of the CEST peaks of [Co(L2)](2+) , [Fe(L2)](2+) , [Ni(L1)](2+) and [Co(L1)](2+) showed that a CEST peak of [Co(L1)](2+) gave the largest CT (-0.66 ppm (o) C(-1) at 4.7 T). NMR spectral and CEST properties of these complexes correspond to coordination complex symmetry as shown by structural data. The [Ni(L1)](2+) and [Co(L1)](2+) complexes have a six-coordinate metal ion bound to the 1-, 4-amide oxygen atoms and four nitrogen atoms of the tetraazamacrocycle. The [Fe(L2)](2+) complex has an unusual eight-coordinate Fe(II) bound to four amide oxygen atoms and four macrocyclic nitrogen atoms. For [Co(L2)](2+) , one structure has seven-coordinate Co(II) with three bound amide pendents and a second structure has a six-coordinate Co(II) with two bound amide pendents.

Influence of solvent chemistry on 1H NMR spectral and relaxation properties of a long-chain ionic surfactant in chloroform-d

1H NMR chemical shift, line width, indirect nuclear splitting value, peak area integration value, and spin–lattice and spin–spin relaxation times at 298 K are compared for low-concentration isotropic solutions of n-octylammonium n-octadecanoate prepared via different techniques and conditions using dried, distilled, and degassed deuterochloroform and the nontreated solvent containing tetramethylsilane. The nature of the variation of observed spectral parameters and relaxation/rotational behavior with chemical composition (presence of oxygen and other paramagnetic species, stabilizer, impurities, and degradation products) of the solvent, history of the solution, and sample containment are analyzed. Relaxation times are interpreted in terms of monomer structure and reorientation and internal rotation modes as a function of atomic position along the n-alkyl chains. Collectively, the relaxation behavior of the surfactant complies with the two-step model of fast picosecond internal rotations of different size segments containing methylene groups separated in timescale from slower large segment and overall molecular tumbling modes of the monomer. Fast motional phenomena do not appear to be appreciably influenced by the chemistry of the solvent in contrast to spectral parameters such as chemical shift and line width of the labile ammonium protons. A model is also presented to explain anomalous variation of the peak area integration value with chemical shift of the ammonium resonance peak.

ChemInform Abstract: From NMR Spectra to Structure

AbstractReview: 190 refs.

Structural biology of cisplatin complexes with cellular targets: the adduct with human copper chaperone atox1 in aqueous solution.

Cisplatin is one of the most used anticancer drugs. Its cellular influx and delivery to target DNA may involve the copper chaperone Atox1 protein. Although the mode of binding is established by NMR spectroscopy measurements in solution-the Pt atom binds to Cys12 and Cys15 while retaining the two ammine groups-the structural determinants of the adduct are not known. Here a structural model by hybrid Car-Parrinello density functional theory-based QM/MM simulations is provided. The platinated site minimally modifies the fold of the protein. The calculated NMR and CD spectral properties are fully consistent with the experimental data. Our in silico/in vitro approach provides, together with previous studies, an unprecedented view into the structural biology of cisplatin-protein adducts.

From NMR spectra to structure

This article discusses the existing methods to correlate NMR parameters describing the high resolution NMR spectra of liquids and solid systems with their structural parameters. Those methods are divided into direct and indirect ones. This article includes two types of direct methods: those based on the Nuclear Overhauser Effect (NOE) contributions to the NMR relaxation and those based on direct measurements of the dipolar couplings using several experimental approaches. Indirect methods are based on the intrinsic dependence of J couplings and shieldings on the atomic coordinates of the atoms in a molecule and its surroundings, requiring complex quantum mechanical calculations to relate NMR spectral properties to molecular and crystal structure. This article discusses how changes in chemical bonding, conformation, and stereo configurations that cause measurable changes in NMR parameters closely related to molecular and crystal structure. The final section provides information about the software and hardware required to perform calculations needed to solve structural problems using high resolution NMR. This article intends to provide molecular structural researchers new to the field of NMR, with an overall panorama of the potential of using high resolution NMR for structure elucidation, when other more traditional techniques are not feasible. To this end and to emphasize the didactic value of this work, after each section a brief conclusion has been added to recap the critical concepts. © 2014 Wiley Periodicals, Inc. Concepts Magn Reson Part A 42A: 261–289, 2013.